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Old 07-24-2015, 04:45 AM   #1
Location: Munich

Join Date: Jul 2015
Posts: 14
Default Read number confusion in tophat2

Dear all,

I am very new to RNA-seq and have plenty of questions. Please be patient if my questions are too stupid. Here's my first one:

When I run tophat2 (2.0.13) on my paired-end Illumina dataset, it reports after "Preparing reads" about 37 Mio kept reads, each left and right, only 20-40k discarded. So far, so good. I understand that this is the Bowtie2 output. Once the run is completed, the "align_summary.txt" is reporting only 2.3 Mio reads each (Input). If it was mapped reads, I'd kind of understand, but input reads? What happened to >90% of the reads?

Since I am in a process of learning-by-doing, I would like to understand what I see here.

Thanks a lot!

Last edited by abisko00; 08-06-2015 at 03:55 AM.
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