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-   -   Tophat - Left Kept Reads (http://seqanswers.com/forums/showthread.php?t=12974)

jkozubek 07-26-2011 11:10 AM

Tophat - Left Kept Reads
 
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 07-27-2011 05:32 AM

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 07-27-2011 05:40 AM

Thanks for comments!


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