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Thanks for your reply, Brian.
I have mRNA Illumina 100bp paired end reads. I have already removed the adapters, but still have that same the high variation on GC% at the 5' end. For the library prep, TruSeq mRNA prep was used, that's why I am guessing I have the same 5' end bias described before on my dataset. Any thoughts?
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BBDuk can trim a set number of bases on the left or right side of a read. However, there are some library-prep protocols that are biased, especially near the read start, and thus have suspicious base-frequency histograms, even though they are correct. So, before you trim, I suggest you map the reads to a reference (even the lowest-quality assembly is OK) to determine whether there is actually a higher error rate in the first X bases of the read. If not, then you should not trim them.
With an assembly, you can determine it like this:
bbmap.sh in=reads.fq mhist=mhist.txt qhist=qhist.txt
This will give you histograms of the average qualities by read position, and match/substitution/insertion/deletion/N rates by read position. That will allow you to determine whether the stated read quality is accurate, and thus whether you need to trim the ends of reads.
If you want to trim a set number of bases on each side, you can use BBDuk's "ftl" (force-trim left) and "ftr" (force-trim right) flags to set the limits of where to trim.
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