Tophat Output Log Files And Reports

Question

[Stevelor]

Hi guys,

there are a lot of log files and stuff in the tophat output directory...but is there any way to get easy statistics such as the number of unique mapped reads...number of repeat mapped reads, unmappablem?! And where can i find some infroamtions about all these log files??

Gives "bowtie.left/rightkeptreads.fixmap.log" the information i am looking for??

In the manual there is nothing about this!

Cheers, Steve!

Answer 1

[Sean Davis]

The simplest way is to use the picard tools or samtools libraries to inform you about the resulting alignments. In particular, you can use samtools flagstat to give you some mapping numbers. If you want to look at duplicates, you'll need to sort and them mark duplicates. You might also look at the picard tool CollectRnaSeqMetrics for a tool specific to RNA-seq.