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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!
abisko00
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!
abisko00