#14 soft clipping

[Anonymous]

Originally created by: ifb... (code.google.com)@gmail.com

What steps will reproduce the problem?
1. mark duplicates

Hi, could be a stupid question but I'm wondering about this issue with duplicates detection:

With fastx_trimmer I did a trimming of the first 10bases for all reads due the fastqc shows a deviation in the per base sequence content in those positions.

I'm confused if this process is the 'soft clipping' you say could produce that mark duplicates don't work correctly. I think that due I'm doing it in all reads, markduplicates will recognizes duplicates because the 11position will be the same for all the PE reads

Thanks in advance, and thanks for your helpful slides,

Iván