Difference between trim galore report and Fastqc pre trimming
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10 months ago
Luern • 0

Hi everyone !

I have a small question about the trim galore report.

I ran my command on 100bp paired RNA-seq data :

trim_galore --dont_gzip --stringency 1 --fastqc --length 15 --paired -o [output] [input_R1] [input_R2]

The report gives me this information :

R1 :

Total reads processed: 28,073,466 Reads with adapters: 17,138,946 (61.1%) Reads written (passing filters): 28,073,466 (100.0%)

R2 :

Total reads processed: 28,073,466 Reads with adapters: 17,165,013 (61.1%) Reads written (passing filters): 28,073,466 (100.0%)

But the problem is that in my fastqc report I don't have as many adapters, a little over 30% for R1 and for R2. R1


Does trim galore sum R1 and R2 in its report?

Thank you very much for your help!

trim galore report • 235 views

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