A new day is coming,whether we like it or not. The question is will you control it,or will it control you?

Chrome(Download)是Google公司开发的一个现代化的网页浏览器，作为三大浏览器之一 它搭载了被称为V8的高效率Javascript引擎。

由于简洁的界面风格 和便捷易用的特点 Chrome的市场份额已经升至45% ，一举超越了Internet Explorer和Mozilla Firefox成为全球第一大浏览器。

作为一个现代化的浏览器，就像智能手机的APP ，每装一个APP，意味着你的手机又多了一个功能。Chrome浏览器也是如此，Google

也提供了网上应用商店供人下载扩展自定义使用。

接下来我会介绍一些大家常用的扩展

ABP广告过滤 / Adblock Plus

超过5000万人使用，适用于 Chrome 的免费的广告拦截器，可阻止所有烦人的广告及恶意软件和跟踪。
享受没有恼人广告的网络世界。

更好的历史记录 / Better History

替换浏览器自带的历史查看页面。本扩展能更好地查看您的历史记录。为查看您的历史记录带来最好的搜索体验，最清晰的界
面和最有帮助的筛选

印象笔记 剪藏 / Evernote Web Clipper

使用印象笔记扩展程序一键保存精彩网页内容到印象笔记帐户。
印象笔记•剪藏，以最快的速度，帮你保存网页、截取屏幕、添加标注、轻松归档，随时随地快速找到所需一切.。

网页截图:注释&批注

捕获整个页面或任何部分，矩形，圆形，箭头，线条和文字，模糊敏感信息，一键上传分享注释。支持PNG和链接。

网易云音乐

不用打开网页，收听网易云音乐，更简单更易用。
网易云音乐Chrome扩展，追求简单体验，不用打开网页不用客户端即可收听网易云音乐，歌单，大牌DJ，我的收藏。与其他
终端同步，更简单，更易用。

重要的网页标签可以固定 防止误关闭(pin tab)

CummeRbund was designed to help simplify the analysis and exploration portion of RNA-Seq data derrived from the output of a differential expression analysis using cuffdiff with the goal of providing fast and intuitive access to your results.

Command:

$ cd cuffdiff
$ R
> library(cummeRbund)
> cuff<-readCufflinks()
> cuff

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.

Cufflinks:

cufflinks [options] <aligned_reads.(sam/bam)>

for example:

$ cufflinks -p 8 -G transcript.gtf --library-type fr-unstranded -o cufflinks_output tophat_out/accepted_hits.bam
  -o/--output-dir              write all output files to this directory              [ default:     ./ ]
  -p/--num-threads             number of threads used during analysis                [ default:      1 ]
  --seed                       value of random number generator seed                 [ default:      0 ]
  -G/--GTF                     quantitate against reference transcript annotations                      
  -g/--GTF-guide               use reference transcript annotation to guide assembly

Cuffmerge:

Use to merge together several Cufflinks assemblies.

cuffmerge [options]* <assembly_GTF_list.txt>

Cuffmerge input files

cuffmerge takes several assembly GTF files from Cufflinks’ as input. Input GTF files must be specified in a “manifest” file listing full paths to the files.

Cuffmerge arguments

<assembly_GTF_list.txt>

Text file “manifest” with a list (one per line) of GTF files that you’d like to merge together into a single GTF file.

Cuffdiff

Use to find significant changes in transcript expression, splicing, and promoter use.

cuffdiff [options]* <transcripts.gtf> \

<sample1_replicate1.sam[,…,sample1_replicateM.sam]> \

<sample2_replicate1.sam[,…,sample2_replicateM.sam]> … \

[sampleN.sam_replicate1.sam[,…,sample2_replicateM.sam]]

Cuffdiff output Files

gene_exp.diff    Gene-level differential expression. Tests differences in the summed FPKM of transcripts sharing each gene_id

cuffdiff过程中同一处理的多个样本间用逗号分隔，不同处理间空格分隔.

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

Usage:

tophat [options]* [reads1_2,...readsN_2]

for example:

tophat -p 8 -G genes.gtf -o C1_R1_thout genome C1_R1_1.fq C1_R1_2.fq
-p 代表线程
-G 代表转录本注释信息
-o 输出文件夹
--segment-length 25 （将redas分成的最小比对片段）
--segment-mismatches 1 （片段比对错配碱基数）
--library-type （是否链特异性）fr-unstranded
—transcriptome-index （转录本的bowtie-index文件）

比对输出文件：

accepted_hits.bam（比对输出）
junctions.bed
insertions.bed and deletions.bed

Sort is a Linux program used for printing lines of input text files and concatenation of all files in sorted order. Sort command takes blank space as field separator and entire Input file as sort key. It is important to notice that sort command don’t actually sort the files but only print the sorted output, until your redirect the output.

This article aims at deep insight of Linux ‘sort’ command with 14 useful practical examples that will show you how to use sort command in Linux.

First we will be creating a text file (tecmint.txt) to execute ‘sort’ command examples. Our working directory is ‘/home/$USER/Desktop/tecmint.

The option ‘-e’ in the below command enables interpretion of backslash and /n tells echo to write each string to a new line.

1

$ echo -e "computer\nmouse\nLAPTOP\ndata\nRedHat\nlaptop\ndebian\nlaptop" > tecmint.txt

Before we start with ‘sort’ lets have a look at the contents of the file and the way it look.

1

$ cat tecmint.txt

Now sort the content of the file using following command.

1

$ sort tecmint.txt

Note: The above command don’t actually sort the contents of text file but only show the sorted output on terminal.

Sort the contents of the file ‘tecmint.txt’ and write it to a file called (sorted.txt) and verify the content by using cat command.

1
2

$ sort tecmint.txt > sorted.txt
$ cat sorted.txt

Now sort the contents of text file ‘tecmint.txt’ in reverse order by using ‘-r’ switch and redirect output to a file ‘reversesorted.txt’. Also check the content listing of the newly created file.

1
2

$ sort -r tecmint.txt > reversesorted.txt
$ cat reversesorted.txt

We are going a create a new file (lsl.txt) at the same location for detailed examples and populate it using the output of ‘ls -l’ for your home directory.

1
2

$ ls -l /home/$USER > /home/$USER/Desktop/tecmint/lsl.txt
$ cat lsl.txt

Now will see examples to sort the contents on the basis of other field and not the default initial characters.

Sort the contents of file ‘lsl.txt’ on the basis of 2nd column (which represents number of symbolic links).

1

$ sort -nk2 lsl.txt

Note: The ‘-n’ option in the above example sort the contents numerically. Option ‘-n’ must be used when we wanted to sort a file on the basis of a column which contains numerical values.

Sort the contents of file ‘lsl.txt’ on the basis of 9th column (which is the name of the files and folders and is non-numeric).

1

$ sort -k9 lsl.txt

It is not always essential to run sort command on a file. We can pipeline it directly on the terminal with actual command.

1

$ ls -l /home/$USER | sort -nk5

Sort and remove duplicates from the text file tecmint.txt. Check if the duplicate has been removed or not.

1
2

$ cat tecmint.txt
$ sort -u tecmint.txt

Rules so far (what we have observed):

1
2
3
4

Lines starting with numbers are preferred in the list and lies at the top until otherwise specified (-r).
Lines starting with lowercase letters are preferred in the list and lies at the top until otherwise specified (-r).
Contents are listed on the basis of occurrence of alphabets in dictionary until otherwise specified (-r).
Sort command by default treat each line as string and then sort it depending upon dictionary occurrence of alphabets (Numeric preferred; see rule – 1) until otherwise specified.

Create a third file ‘lsla.txt’ at the current location and populate it with the output of ‘ls -lA’ command.

1
2

$ ls -lA /home/$USER > /home/$USER/Desktop/tecmint/lsla.txt
$ cat lsla.txt

Those having understanding of ‘ls’ command knows that ‘ls -lA’=’ls -l’ + Hidden files. So most of the contents on these two files would be same.

Sort the contents of two files on standard output in one go.

1

$ sort lsl.txt lsla.txt

Notice the repetition of files and folders.

Now we can see how to sort, merge and remove duplicates from these two files.

1

$ sort -u lsl.txt lsla.txt

Notice that duplicates has been omitted from the output. Also, you can write the output to a new file by redirecting the output to a file.

We may also sort the contents of a file or the output based upon more than one column. Sort the output of ‘ls -l’ command on the basis of field 2,5 (Numeric) and 9 (Non-Numeric).

1

$ ls -l /home/$USER | sort -t "," -nk2,5 -k9

That’s all for now. In the next article we will cover a few more examples of ‘sort’ command in detail for you. Till then stay tuned and connected to Tecmint. Keep sharing. Keep commenting. Like and share us and help us get spread.

More info: sort

Here you’ll find a short description and examples of how to use the FASTX-toolkit from the command line.

Command Line Arguments

Most tools show usage information with -h.
Tools can read from STDIN and write to STDOUT, or
from a specific input file (-i) and specific output file (-o).
Tools can operate silently (producing no output if everything was OK), or
print a short summary (-v).
If output goes to STDOUT, the summary will be printed to STDERR.
If output goes to a file, the summary will be printed to STDOUT.
Some tools can compress the output with GZIP (-z).

FASTQ-to-FASTA

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

$ fastq_to_fasta -h
usage: fastq_to_fasta [-h] [-r] [-n] [-v] [-z] [-i INFILE] [-o OUTFILE]

version 0.0.6
   [-h]         = This helpful help screen.
   [-r]         = Rename sequence identifiers to numbers.
   [-n]         = keep sequences with unknown (N) nucleotides.
		  Default is to discard such sequences.
   [-v]         = Verbose - report number of sequences.
		  If [-o] is specified,  report will be printed to STDOUT.
		  If [-o] is not specified (and output goes to STDOUT),
		  report will be printed to STDERR.
   [-z]         = Compress output with GZIP.
   [-i INFILE]  = FASTA/Q input file. default is STDIN.
   [-o OUTFILE] = FASTA output file. default is STDOUT.

FASTX Statistics

$ fastx_quality_stats -h
usage: fastx_quality_stats [-h] [-i INFILE] [-o OUTFILE]

version 0.0.6 (C) 2008 by Assaf Gordon (gordon@cshl.edu)
   [-h] = This helpful help screen.
   [-i INFILE]  = FASTA/Q input file. default is STDIN.
                  If FASTA file is given, only nucleotides
          distribution is calculated (there's no quality info).
   [-o OUTFILE] = TEXT output file. default is STDOUT.

The output TEXT file will have the following fields (one row per column):
    column    = column number (1 to 36 for a 36-cycles read solexa file)
    count   = number of bases found in this column.
    min     = Lowest quality score value found in this column.
    max     = Highest quality score value found in this column.
    sum     = Sum of quality score values for this column.
    mean    = Mean quality score value for this column.
    Q1    = 1st quartile quality score.
    med    = Median quality score.
    Q3    = 3rd quartile quality score.
    IQR    = Inter-Quartile range (Q3-Q1).
    lW    = 'Left-Whisker' value (for boxplotting).
    rW    = 'Right-Whisker' value (for boxplotting).
    A_Count    = Count of 'A' nucleotides found in this column.
    C_Count    = Count of 'C' nucleotides found in this column.
    G_Count    = Count of 'G' nucleotides found in this column.
    T_Count    = Count of 'T' nucleotides found in this column.
    N_Count = Count of 'N' nucleotides found in this column.
    max-count = max. number of bases (in all cycles)

FASTQ Quality Chart

$ fastq_quality_boxplot_graph.sh -h
Solexa-Quality BoxPlot plotter
Generates a solexa quality score box-plot graph 

Usage: /usr/local/bin/fastq_quality_boxplot_graph.sh [-i INPUT.TXT] [-t TITLE] [-p] [-o OUTPUT]

  [-p]           - Generate PostScript (.PS) file. Default is PNG image.
  [-i INPUT.TXT] - Input file. Should be the output of "solexa_quality_statistics" program.
  [-o OUTPUT]    - Output file name. default is STDOUT.
  [-t TITLE]     - Title (usually the solexa file name) - will be plotted on the graph.

FASTA/Q Nucleotide Distribution

$ fastx_nucleotide_distribution_graph.sh -h
FASTA/Q Nucleotide Distribution Plotter

Usage: /usr/local/bin/fastx_nucleotide_distribution_graph.sh [-i INPUT.TXT] [-t TITLE] [-p] [-o OUTPUT]

  [-p]           - Generate PostScript (.PS) file. Default is PNG image.
  [-i INPUT.TXT] - Input file. Should be the output of "fastx_quality_statistics" program.
  [-o OUTPUT]    - Output file name. default is STDOUT.
  [-t TITLE]     - Title - will be plotted on the graph.

FASTA/Q Clipper

$ fastx_clipper -h
usage: fastx_clipper [-h] [-a ADAPTER] [-D] [-l N] [-n] [-d N] [-c] [-C] [-o] [-v] [-z] [-i INFILE] [-o OUTFILE]

version 0.0.6
   [-h]         = This helpful help screen.
   [-a ADAPTER] = ADAPTER string. default is CCTTAAGG (dummy adapter).
   [-l N]       = discard sequences shorter than N nucleotides. default is 5.
   [-d N]       = Keep the adapter and N bases after it.
          (using '-d 0' is the same as not using '-d' at all. which is the default).
   [-c]         = Discard non-clipped sequences (i.e. - keep only sequences which contained the adapter).
   [-C]         = Discard clipped sequences (i.e. - keep only sequences which did not contained the adapter).
   [-k]         = Report Adapter-Only sequences.
   [-n]         = keep sequences with unknown (N) nucleotides. default is to discard such sequences.
   [-v]         = Verbose - report number of sequences.
          If [-o] is specified,  report will be printed to STDOUT.
          If [-o] is not specified (and output goes to STDOUT),
          report will be printed to STDERR.
   [-z]         = Compress output with GZIP.
   [-D]        = DEBUG output.
   [-i INFILE]  = FASTA/Q input file. default is STDIN.
   [-o OUTFILE] = FASTA/Q output file. default is STDOUT.

FASTA/Q Renamer

$ fastx_renamer -h
usage: fastx_renamer [-n TYPE] [-h] [-z] [-v] [-i INFILE] [-o OUTFILE]
Part of FASTX Toolkit 0.0.10 by A. Gordon (gordon@cshl.edu)

   [-n TYPE]    = rename type:
          SEQ - use the nucleotides sequence as the name.
          COUNT - use simply counter as the name.
   [-h]         = This helpful help screen.
   [-z]         = Compress output with GZIP.
   [-i INFILE]  = FASTA/Q input file. default is STDIN.
   [-o OUTFILE] = FASTA/Q output file. default is STDOUT.

FASTA/Q Trimmer

$ fastx_trimmer -h
usage: fastx_trimmer [-h] [-f N] [-l N] [-z] [-v] [-i INFILE] [-o OUTFILE]

version 0.0.6
   [-h]         = This helpful help screen.
   [-f N]       = First base to keep. Default is 1 (=first base).
   [-l N]       = Last base to keep. Default is entire read.
   [-z]         = Compress output with GZIP.
   [-i INFILE]  = FASTA/Q input file. default is STDIN.
   [-o OUTFILE] = FASTA/Q output file. default is STDOUT.

FASTA/Q Collapser

$ fastx_collapser -h
usage: fastx_collapser [-h] [-v] [-i INFILE] [-o OUTFILE]

version 0.0.6
   [-h]         = This helpful help screen.
   [-v]         = verbose: print short summary of input/output counts
   [-i INFILE]  = FASTA/Q input file. default is STDIN.
   [-o OUTFILE] = FASTA/Q output file. default is STDOUT.

FASTQ/A Artifacts Filter

$ fastx_artifacts_filter -h
usage: fastq_artifacts_filter [-h] [-v] [-z] [-i INFILE] [-o OUTFILE]

version 0.0.6
   [-h]         = This helpful help screen.
   [-i INFILE]  = FASTA/Q input file. default is STDIN.
   [-o OUTFILE] = FASTA/Q output file. default is STDOUT.
   [-z]         = Compress output with GZIP.
   [-v]         = Verbose - report number of processed reads.
          If [-o] is specified,  report will be printed to STDOUT.
          If [-o] is not specified (and output goes to STDOUT),
          report will be printed to STDERR.

FASTQ Quality Filter

$ fastq_quality_filter -h
usage: fastq_quality_filter [-h] [-v] [-q N] [-p N] [-z] [-i INFILE] [-o OUTFILE]

version 0.0.6
   [-h]         = This helpful help screen.
   [-q N]       = Minimum quality score to keep.
   [-p N]       = Minimum percent of bases that must have [-q] quality.
   [-z]         = Compress output with GZIP.
   [-i INFILE]  = FASTA/Q input file. default is STDIN.
   [-o OUTFILE] = FASTA/Q output file. default is STDOUT.
   [-v]         = Verbose - report number of sequences.
          If [-o] is specified,  report will be printed to STDOUT.
          If [-o] is not specified (and output goes to STDOUT),
          report will be printed to STDERR.

FASTQ/A Reverse Complement

$ fastx_reverse_complement -h
usage: fastx_reverse_complement [-h] [-r] [-z] [-v] [-i INFILE] [-o OUTFILE]

version 0.0.6
   [-h]         = This helpful help screen.
   [-z]         = Compress output with GZIP.
   [-i INFILE]  = FASTA/Q input file. default is STDIN.
   [-o OUTFILE] = FASTA/Q output file. default is STDOUT.

FASTA Formatter

$ fasta_formatter -h
usage: fasta_formatter [-h] [-i INFILE] [-o OUTFILE] [-w N] [-t] [-e]
Part of FASTX Toolkit 0.0.7 by gordon@cshl.edu

   [-h]         = This helpful help screen.
   [-i INFILE]  = FASTA/Q input file. default is STDIN.
   [-o OUTFILE] = FASTA/Q output file. default is STDOUT.
   [-w N]       = max. sequence line width for output FASTA file.
          When ZERO (the default), sequence lines will NOT be wrapped -
          all nucleotides of each sequences will appear on a single 
          line (good for scripting).
   [-t]         = Output tabulated format (instead of FASTA format).
          Sequence-Identifiers will be on first column,
          Nucleotides will appear on second column (as single line).
   [-e]         = Output empty sequences (default is to discard them).
          Empty sequences are ones who have only a sequence identifier,
          but not actual nucleotides.

Input Example:
   >MY-ID
   AAAAAGGGGG
   CCCCCTTTTT
   AGCTN

Output example with unlimited line width [-w 0]:
   >MY-ID
   AAAAAGGGGGCCCCCTTTTTAGCTN

Output example with max. line width=7 [-w 7]:
   >MY-ID
   AAAAAGG
   GGGTTTT
   TCCCCCA
   GCTN

Output example with tabular output [-t]:
   MY-ID    AAAAAGGGGGCCCCCTTTTAGCTN

example of empty sequence:
(will be discarded unless [-e] is used)
  >REGULAR-SEQUENCE-1
  AAAGGGTTTCCC
  >EMPTY-SEQUENCE
  >REGULAR-SEQUENCE-2
  AAGTAGTAGTAGTAGT
  GTATTTTATAT

FASTA Nucleotides Changer

$ fasta_nucleotide_changer -h
usage: fasta_nucleotide_changer [-h] [-z] [-v] [-i INFILE] [-o OUTFILE] [-r] [-d]

version 0.0.7
   [-h]         = This helpful help screen.
   [-z]         = Compress output with GZIP.
   [-v]         = Verbose mode. Prints a short summary.
          with [-o], summary is printed to STDOUT.
          Otherwise, summary is printed to STDERR.
   [-i INFILE]  = FASTA/Q input file. default is STDIN.
   [-o OUTFILE] = FASTA/Q output file. default is STDOUT.
   [-r]         = DNA-to-RNA mode - change T's into U's.
   [-d]         = RNA-to-DNA mode - change U's into T's.

FASTA Clipping Histogram

$ fasta_clipping_histogram.pl
Create a Linker Clipping Information Histogram

usage: fasta_clipping_histogram.pl INPUT_FILE.FA OUTPUT_FILE.PNG

    INPUT_FILE.FA   = input file (in FASTA format, can be GZIPped)
    OUTPUT_FILE.PNG = histogram image

FASTX Barcode Splitter

$ fastx_barcode_splitter.pl
Barcode Splitter, by Assaf Gordon (gordon@cshl.edu), 11sep2008

This program reads FASTA/FASTQ file and splits it into several smaller files,
Based on barcode matching.
FASTA/FASTQ data is read from STDIN (format is auto-detected.)
Output files will be writen to disk.
Summary will be printed to STDOUT.

usage: /usr/local/bin/fastx_barcode_splitter.pl --bcfile FILE --prefix PREFIX [--suffix SUFFIX] [--bol|--eol] 
     [--mismatches N] [--exact] [--partial N] [--help] [--quiet] [--debug]

Arguments:

--bcfile FILE    - Barcodes file name. (see explanation below.)
--prefix PREFIX    - File prefix. will be added to the output files. Can be used
          to specify output directories.
--suffix SUFFIX    - File suffix (optional). Can be used to specify file
          extensions.
--bol        - Try to match barcodes at the BEGINNING of sequences.
          (What biologists would call the 5' end, and programmers
          would call index 0.)
--eol        - Try to match barcodes at the END of sequences.
          (What biologists would call the 3' end, and programmers
          would call the end of the string.)
          NOTE: one of --bol, --eol must be specified, but not both.
--mismatches N    - Max. number of mismatches allowed. default is 1.
--exact        - Same as '--mismatches 0'. If both --exact and --mismatches 
          are specified, '--exact' takes precedence.
--partial N    - Allow partial overlap of barcodes. (see explanation below.)
          (Default is not partial matching)
--quiet        - Don't print counts and summary at the end of the run.
          (Default is to print.)
--debug        - Print lots of useless debug information to STDERR.
--help        - This helpful help screen.

Example (Assuming 's_2_100.txt' is a FASTQ file, 'mybarcodes.txt' is 

the barcodes file):

   $ cat s_2_100.txt | /usr/local/bin/fastx_barcode_splitter.pl --bcfile mybarcodes.txt --bol --mismatches 2 \
    --prefix /tmp/bla_ --suffix ".txt"

Barcode file format
-------------------
Barcode files are simple text files. Each line should contain an identifier 
(descriptive name for the barcode), and the barcode itself (A/C/G/T), 
separated by a TAB character. Example:

    #This line is a comment (starts with a 'number' sign)
    BC1 GATCT
    BC2 ATCGT
    BC3 GTGAT
    BC4 TGTCT

For each barcode, a new FASTQ file will be created (with the barcode's 
identifier as part of the file name). Sequences matching the barcode 
will be stored in the appropriate file.

Running the above example (assuming "mybarcodes.txt" contains the above 
barcodes), will create the following files:
    /tmp/bla_BC1.txt
    /tmp/bla_BC2.txt
    /tmp/bla_BC3.txt
    /tmp/bla_BC4.txt
    /tmp/bla_unmatched.txt
The 'unmatched' file will contain all sequences that didn't match any barcode.

Barcode matching
----------------

** Without partial matching:

Count mismatches between the FASTA/Q sequences and the barcodes.
The barcode which matched with the lowest mismatches count (providing the
count is small or equal to '--mismatches N') 'gets' the sequences.

Example (using the above barcodes):
Input Sequence:
    GATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG

Matching with '--bol --mismatches 1':
   GATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG
   GATCT (1 mismatch, BC1)
   ATCGT (4 mismatches, BC2)
   GTGAT (3 mismatches, BC3)
   TGTCT (3 mismatches, BC4)

This sequence will be classified as 'BC1' (it has the lowest mismatch count).
If '--exact' or '--mismatches 0' were specified, this sequence would be 
classified as 'unmatched' (because, although BC1 had the lowest mismatch count,
it is above the maximum allowed mismatches).

Matching with '--eol' (end of line) does the same, but from the other side
of the sequence.

** With partial matching (very similar to indels):

Same as above, with the following addition: barcodes are also checked for
partial overlap (number of allowed non-overlapping bases is '--partial N').

Example:
Input sequence is ATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG
(Same as above, but note the missing 'G' at the beginning.)

Matching (without partial overlapping) against BC1 yields 4 mismatches:
   ATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG
   GATCT (4 mismatches)

Partial overlapping would also try the following match:
   -ATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG
   GATCT (1 mismatch)

Note: scoring counts a missing base as a mismatch, so the final
mismatch count is 2 (1 'real' mismatch, 1 'missing base' mismatch).
If running with '--mismatches 2' (meaning allowing upto 2 mismatches) - this 
seqeunce will be classified as BC1.

Example: FASTQ Information

Genrating Quality Information on BC54.fq:

$ fastx_quality_stats -i BC54.fq -o bc54_stats.txt
$ fastq_quality_boxplot_graph.sh -i bc54_stats.txt -o bc54_quality.png -t “My Library”
$ fastx_nucleotide_distribution_graph.sh -i bc54_stats.txt -o bc54_nuc.png -t “My Library”

Example: FASTQ/A Manipulation

Common pre-processing work-flow:

Covnerting FASTQ to FASTA
Clipping the Adapter/Linker
Trimming to 27nt (if you’re analyzing miRNAs, for example)
Collapsing the sequences
Plotting the clipping results

Using the FASTX-toolkit from the command line:

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18

$ fastq_to_fasta -v -n -i BC54.fq -o BC54.fa
Input: 100000 reads.
Output: 100000 reads.
$ fastx_clipper -v -i BC54.fa -a CTGTAGGCACCATCAATTCGTA -o BC54.clipped.fa
Clipping Adapter: CTGTAGGCACCATCAATTCGTA
Min. Length: 15
Input: 100000 reads.
Output: 92533 reads.
discarded 468 too-short reads.
discarded 6939 adapter-only reads.
discarded 60 N reads.
$ fastx_trimmer -v -f 1 -l 27 -i BC54.clipped.fa -o BC54.trimmed.fa
Trimming: base 1 to 27
Input: 92533 reads.
Output: 92533 reads.
$ fastx_collapser -v -i BC54.trimmed.fa -o BC54.collapsed.fa
Collapsd 92533 reads into 36431 unique sequences.
$ fasta_clipping_histogram.pl BC54.collapsed.fa bc54_clipping.png

Mapping (or any other kind of analysis) of the Clipped + Collapsed FASTA file will be:

quicker - each unique sequence appears only once in the FASTA file.
more accurate - the Adapter/Linker sequence was removed from the 3’ end, and will affect the mapping results.

Welcome to Hexo! This is your very first post. Check documentation for more info. If you get any problems when using Hexo, you can find the answer in troubleshooting or you can ask me on GitHub.

Quick Start

Create a new post

1

$ hexo new "My New Post"

More info: Writing

Run server

1

$ hexo server

More info: Server

Generate static files

1

$ hexo generate

More info: Generating

Deploy to remote sites

1

$ hexo deploy

More info: Deployment

Let us start new year with these Unix command line tricks to increase productivity at the Terminal. I have found them over the years and I’m now going to share with you.

Deleting a HUGE file

I had a huge log file 200GB I need to delete on a production web server. My rm and ls command was crashed and I was afraid that the system to a crawl with huge disk I/O load. To remove a HUGE file, enter:

1
2
3
4
5
6

> /path/to/file.log
# or use the following syntax
: > /path/to/file.log
 
# finally delete it 
rm /path/to/file.log

Want to cache console output?

Try the script command line utility to create a typescript of everything printed on your terminal.

1

script my.terminal.session

Type commands:

1
2
3

ls
date
sudo service foo stop

To exit (to end script session) type exit or logout or press control-D

1

exit

To view type:

1
2
3

more my.terminal.session
less my.terminal.session
cat my.terminal.session

Restoring deleted /tmp folder

As my journey continues with Linux and Unix shell, I made a few mistakes. I accidentally deleted /tmp folder. To restore it all you have to do is:

1
2
3
4

mkdir /tmp
chmod 1777 /tmp
chown root:root /tmp
ls -ld /tmp

Locking a directory

For privacy of my data I wanted to lock down /downloads on my file server. So I ran:

1

chmod 0000 /downloads

The root user can still has access and ls and cd commands will not work. To go back:

1

chmod 0755 /downloads

Password protecting file in vim text editor

Afraid that root user or someone may snoop into your personal text files? Try password protection to a file in vim, type:

1
2
3
4
5
6
7
8
9
10

vim +X filename
``` 
Or, before quitting in vim use :X vim command to encrypt your file and vim will prompt for a password.

### Clear gibberish all over the screen

Just type:

``` bash 
reset

Becoming human

Pass the -h or -H (and other options) command line option to GNU or BSD utilities to get output of command commands like ls, df, du, in human-understandable formats:

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22

ls -lh
# print sizes in human readable format (e.g., 1K 234M 2G)
df -h
df -k
# show output in bytes, KB, MB, or GB
free -b
free -k
free -m
free -g
# print sizes in human readable format (e.g., 1K 234M 2G)
du -h
# get file system perms in human readable format
stat -c %A /boot
# compare human readable numbers
sort -h -a file
# display the CPU information in human readable format on a Linux
lscpu
lscpu -e
lscpu -e=cpu,node
# Show the  size of each file but in a more human readable way
tree -h
tree -h /boot

Show information about known users in the Linux based system

Just type:

1
2
3
4
5

## linux version ##
lslogins
 
## BSD version ##
logins

Sample outputs:

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29

UID USER      PWD-LOCK PWD-DENY LAST-LOGIN GECOS
  0 root             0        0   22:37:59 root
  1 bin              0        1            bin
  2 daemon           0        1            daemon
  3 adm              0        1            adm
  4 lp               0        1            lp
  5 sync             0        1            sync
  6 shutdown         0        1 2014-Dec17 shutdown
  7 halt             0        1            halt
  8 mail             0        1            mail
 10 uucp             0        1            uucp
 11 operator         0        1            operator
 12 games            0        1            games
 13 gopher           0        1            gopher
 14 ftp              0        1            FTP User
 27 mysql            0        1            MySQL Server
 38 ntp              0        1
 48 apache           0        1            Apache
 68 haldaemon        0        1            HAL daemon
 69 vcsa             0        1            virtual console memory owner
 72 tcpdump          0        1
 74 sshd             0        1            Privilege-separated SSH
 81 dbus             0        1            System message bus
 89 postfix          0        1
 99 nobody           0        1            Nobody
173 abrt             0        1
497 vnstat           0        1            vnStat user
498 nginx            0        1            nginx user
499 saslauth         0        1            "Saslauthd user"

How do I fix mess created by accidentally untarred files in the current dir?

So I accidentally untar a tarball in /var/www/html/ directory instead of /home/projects/www/current. It created mess in /var/www/html/. The easiest way to fix this mess:

1
2

cd /var/www/html/
/bin/rm -f "$(tar ztf /path/to/file.tar.gz)"

Confused on a top command output?

Seriously, you need to try out htop instead of top:

1

sudo htop

Want to run the same command again?

Just type !!. For example:

1
2
3
4
5
6
7

/myhome/dir/script/name arg1 arg2
 
# To run the same command again 
!!
 
## To run the last command again as root user
sudo !!

The !! repeats the most recent command. To run the most recent command beginning with “foo”:

1
2
3

!foo
# Run the most recent command beginning with "service" as root
sudo !service

The !$ use to run command with the last argument of the most recent command:

1
2
3
4
5
6
7
8
9

# Edit nginx.conf
sudo vi /etc/nginx/nginx.conf
 
# Test nginx.conf for errors
/sbin/nginx -t -c /etc/nginx/nginx.conf
 
# After testing a file with "/sbin/nginx -t -c /etc/nginx/nginx.conf", you
# can edit file again with vi
sudo vi !$

Get a reminder you when you have to leave

If you need a reminder to leave your terminal, type the following command:

1

leave +hhmm

Where,

hhmm - The time of day is in the form hhmm where hh is a time in hours (on a 12 or 24 hour clock), and mm are minutes. All times are converted to a 12 hour clock, and assumed to be in the next 12 hours.

Home sweet home

Want to go the directory you were just in? Run:

1

cd -

Need to quickly return to your home directory? Enter:

1

cd

The variable CDPATH defines the search path for the directory containing directories:

1

export CDPATH=/var/www:/nas10

Now, instead of typing cd /var/www/html/ I can simply type the following to cd into /var/www/html path:

1

cd html

Editing a file being viewed with less pager

To edit a file being viewed with less pager, press v. You will have the file for edit under $EDITOR:

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39

less *.c
less foo.html
## Press v to edit file ##
## Quit from editor and you would return to the less pager again ##
``` bash
### List all files or directories on your system

To see all of the directories on your system, run:
``` bash
find / -type d | less
 
# List all directories in your $HOME
find $HOME -type d -ls | less
``` 
To see all of the files, run:
``` bash
find / -type f | less
 
# List all files in your $HOME
find $HOME -type f -ls | less
``` 
### Build directory trees in a single command

You can create directory trees one at a time using mkdir command by passing the -p option:
``` bash
mkdir -p /jail/{dev,bin,sbin,etc,usr,lib,lib64}
ls -l /jail/
``` 
### Copy file into multiple directories

Instead of running:
``` bash
cp /path/to/file /usr/dir1
cp /path/to/file /var/dir2
cp /path/to/file /nas/dir3
``` 
Run the following command to copy file into multiple dirs:
``` bash
echo /usr/dir1 /var/dir2 /nas/dir3 |  xargs -n 1 cp -v /path/to/file

Creating a shell function is left as an exercise for the reader

Quickly find differences between two directories

The diff command compare files line by line. It can also compare two directories:

1
2
3
4

ls -l /tmp/r
ls -l /tmp/s
# Compare two folders using diff ##
diff /tmp/r/ /tmp/s/

Text formatting

You can reformat each paragraph with fmt command. In this example, I’m going to reformat file by wrapping overlong lines and filling short lines:

1

fmt file.txt

You can also split long lines, but do not refill i.e. wrap overlong lines, but do not fill short lines:

1

fmt -s file.txt

See the output and write it to a file

Use the tee command as follows to see the output on screen and also write to a log file named my.log:

1

mycoolapp arg1 arg2 input.file | tee my.log

The tee command ensures that you will see mycoolapp output on on the screen and to a file same time.

More info: Unix Command