Regarding the accepted_hits.sam, left_kept_reads.fq.candidate_hits.sam, and the left_kept_reads.fq files. How do I interpret their meaning? I'm asking because we'd like to calculate what percentage of the original reads are contributing to the calculated RPKM values I get in the Tophat output. I assume the accepted_hits.sam file is literally all of the successfully aligned source reads from Bowtie but how should I interpret these other files?
Thanks.
Thanks.
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