I have trimmed adapters (from read start) using cutadapt, however fastqc shows that there is some sequence composition bias in the end of long reads.
My question - how could this happen (probably it's not biological) and should I cut end of such reads? If so, how far should I cut?
1 answer
Run fastqc with the -nogroup option to see more precisely what is going on - the image above uses 5 wide bins.
When you cut adapters make sure to also include whatever extra base might be ligated onto the sequence. For example during Illumina sequencing there is an extra A overhang that is not technically part of the adapter yet should be added to the adapter sequence.
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written
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Istvan Albert
Most tools can be told to cut a fixed number of bases from either end but it would good to identify why such an enrichment would be there and whether that has any significance
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written
by
Istvan Albert
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