Hi,
I am working with a previously preprocessed (trimmed, and adapters are removed) miRNA-seq data. On the per base sequence quality plot there are some weird drops in quality at the 2nd, 7th, 14th base. 
This pattern can be seen in a in about half of the samples.
What can be the cause of it? Should I trim the 5' end?
About the 3' end of the reads: there are just a few reads longer than 30 bp, this yields the low quality and large deviation at the 3' end, I am planning on setting the max read length to 30 or 35 bp. 
Thanks!
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written
by
kim.malek90 •
1 answer
If this is really an miRNA dataset then you are probably interested in first ~20-25 bp or so anyway.
Since the length of (some of) reads seems to be 45+ this data either may not be trimmed or if trimmed has other reads that don't have miRNA (and thus should be removed as well).
some weird drops in quality at the 2nd, 7th, 14th base
That could just be because of perceived low nucleotide diversity (that cycle has all A's for example) by the sequencer.
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