TopHat

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

本文固定链接:http://tiramisutes.github.io/2015/07/25/TopHat.html 转载请注明出处!

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