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Old 07-26-2011, 11:10 AM   #1
jkozubek
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Location: Boston University

Join Date: Mar 2011
Posts: 18
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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