Hi all I am dealing with RNA Seq data and I have raw read counts of 13 samples. I want to have a read frequency table as I want to see the most abundant miRNAs among list of thousands of miRNAs produced after mapping step . Is there any way to do it in R/ Bioconductor? Also I need a little clarification on most abundant miRNA and most expressed miRNA. Aren’t they same ?
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written
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vkgaur25 •
1 answer
You're looking for TPMs, which are "transcripts per million". You can search this site for how to get that from count data. However, there's little point in doing that. miRNAs have a fairly tight length distribution, so you can just cut to the chase and use the miRNAs with the highest counts.
The most highly expressed miRNA is also the most abundant, the two concepts are identical unless one means "transcribed" when one writes "expressed" (one should then write that instead).
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Please post some example data and expected output/format. In general, most of the software output the statistics. Look at logs.