All of them are 38-40 nt long after adapter trimming. Does anyone have idea how to deal with differential expression analysis with these reads using CLC bio? Since these reads are longer than expected mature miRNA length, I have problem with setting up cut of mismatch bases to extract annotation. It looks like CLC Bio does not have option to customize mismatch only within mature or flanking region. Or any additional tools for differential expression ?
This is very strange case:
Please, ensure you trimmed both 5' and 3' adapters.
I would map some of those reads to have a better idea what I am dealing with as they may be rRNA derived small RNAs. If they correctly map to some of the sequences in your reference genome. You may infer what is going on with those reads. It could be an error in library preparation, or RNA extraction RNA contamination, etc.
Are you using Illumina's TruSeq Small RNA kit?
The illumina adapters are 60bp (120bp total) each so they may not be fully trimmed, but it is not likely that you missed one or the other.
Hi Naholi and Seth,
Thank you for your answers. I figured it now and results look promising.
Glad to hear that, can you tell me what the problem was?
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