Tophat - Left Kept Reads

[jkozubek]

Hello:

I am wondering if Tophat generates a file of seq direct to the genome, prior to doing its mapping to the exon-exon junctions. I am hoping it does, such that i don't need to do a separate Bowtie run. Is that what the "left_kept_reads" file is, mapping reads that don't need exon-exon junctions to find the genome?

Jim

[chenyao]

I think in tophat_out files, "left_kept_reads" is mapped by bowtie, "left_kept_reads_seq1"(forget the name,the second one) is mapped by the rest reads which failed by bowtie.

[jkozubek]

Thanks for comments!