Entering edit mode
2.9 years ago
Georgia
•
0
Hello, I have a doubt about my trimming. I have paired end WGBS data, my R1 has masked adapters while my R2 present specific sequence of adapter. I am using trimgalore to trim the R2 but in paired end mode, so in theory is also trimming my R1. I was expecting that R1 will be not trimmed because of masked Ns, but actually the R1 report tells there were around 20% of reads with adapters. Do I have to run trimgalore in single end mode just for R2? does the weird trimmng of R1 affecting the further analysis??
thank you!
While this is not generally recommended you could trim just R2 reads using trimgalore, if you just wanted to trim that end. Then use
repair.shfrom BBMap suite to retrieve corresponding R1 reads to remake a synced data set.