Hi~ I'm working on some WGBS data now.
After quality and adapter trimming, Sequence Duplication Levels and Per sequence GC content still cannot pass . In Per sequence GC content, the read peak is higher than theoretical distibution. Is this ok ?
Thank you very much if you can provide some help !
Here are some pictures from FastQC after trimming.
There is a small fluctuation at the first few bases.Should I trim it ? At the end, the sharp decrease of A at the last position is a result of removing the adapter sequence very stringently, i.e. even a single trailing A at the end is removed.
Should I deduplicate sequence during quality control ( before mapping ) or filtering reads after alignments using deduplicate_bismark ?
1 answer
Don't worry too much about FastQC reports. They are very conservative. It's nearly impossible to have them all pass. You should manually look at the report and see if each section makes sense.
See previous discussion here about FastQC: FastQ quality check : what can we correct ?
And you can use deduplicate_bismark to remove duplicates, which is convenient if you are using Bismark for everything else.
Correct, there's no reason to bother deduplicating before alignment.
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