--combined-output generates strange GC% distribution in fastqc reports about adapterremoval HOT 4 CLOSED

After eliminating all sequences with just 'N' in both R1 and R2 of the combined output files, I again obtained normal curves for GC content, so that explains the issue.

from adapterremoval.

Dear Clara,

Thank you for the detailed error report and for the followup.
I am able to reproduce the problem, but unfortunately there does not seem to be an easy way to filter reads in FASTQC. So I am afraid that you'll have to filter your reads manually, before running FASTQC.

To answer your second question, the --collapse function works based purely on the reads themselves, so there is a risk of reads pairs overlapping highly repetitive regions being merged by mistake. This is an inherent problem with any such tool. I have not investigated how big this problem is, but you might be able to mitigate it by increasing the minimum required overlap using the --minalignmentlength option, which defaults to requiring at least 11 bps over overlap before collapsing a pair of reads.

Best,
Mikkel

from adapterremoval.

Hi Mikkel,

Thanks a lot for your insights. I don't think it's a very big issue that the GC% is a bit deviated in FastQC reports, now that it's clear where the pattern is coming from. Thank you for maintaining AdapterRemoval, it's always worked very well for me!

from adapterremoval.

I am glad to hear that AdapterRemoval has been useful to you!
Don't hesitate to open another issue, if you run into other problems or if you have other questions.

Best,
Mikkel

from adapterremoval.