search

BosingerLab / BALDR

MIT License
7 stars 8 forks source link

Suggest quality filtering in Trimmomatic #7

Open scharch opened 5 years ago

scharch commented 5 years ago

I am seeing intermittent cases where Trimmomatic is failing to remove adapter sequences properly. In the attached alignment, it is assembling 4 separate contigs from what is clearly the same VDJ rearrangement --the problem is adapter contamination. When I add LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 to the Trimmomatic command line, it gets correctly assembled into a single contig spanning the entire amplicon, as seen in the attachment.

quality_example.txt

amit-upadhyay commented 5 years ago

Thank you for the suggestion. I will incorporate these changes.