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Old 07-26-2011, 11:10 AM   #1
jkozubek
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Default 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
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Old 07-27-2011, 05:32 AM   #2
chenyao
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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.
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Old 07-27-2011, 05:40 AM   #3
jkozubek
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Thanks for comments!
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