Question

low counts from microRNA seq

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abhay.kanodia • 0

@abhaykanodia-23398

Last seen 23 months ago

United States

I have 24 samples on which smallRNA seq was performed, most of the genes have 0 counts o0r very low counts. Is this normal for microRNA seq? Attached a screenshot of .csv file with count matrix.

I have three different treatment groups. Due to this, all the treatment groups have same differentially expressed microRNAs but the log2fold change is different. Thank you!

enter image description here

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# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

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DESeq2 microRNA HTSeq • 1.3k views

ADD COMMENT • link 24 months ago abhay.kanodia • 0

score 1 · Answer 1 · 2022-12-24

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ATpoint ★ 4.6k

@atpoint-13662

Last seen 21 hours ago

Germany

The support site is intended to help with technical problems towards Bioconductor packages. This is not a DESeq2 problem. Better communities would be biostars.org or a suitable sub-reddit. In any case smallRNA-seq sequences small RNA, your table shows some protein-coding genes, these would naturally not be captured here. Check existing pipelines how to process these sorts of data, for example https://nf-co.re/smrnaseq and others to be found via your favourit search engine.

ADD COMMENT • link 24 months ago ATpoint ★ 4.6k

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Hi @ATpoint,

Thanks for your comments. However, when I perform DESeq2, I get the following results even after filtering for miRNA, not sure if its a DESeq2 problem or not. Only 45 miRNAs have some log2foldchange value in it, the rest do not.

enter image description here

ADD REPLY • link 24 months ago abhay.kanodia • 0

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Basemean of zero means these genes have no counts, it's something upstream of DESeq2.

ADD REPLY • link 24 months ago ATpoint ★ 4.6k

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Thanks so much @atpoint. So that means all the miroRNAs should have had some count value? Its unusual to have a countmatrix with such counts for microRNA sequencing?

ADD REPLY • link 24 months ago abhay.kanodia • 0

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It's the wrong forum here, please ask somewhere else (biostars or reddit), adding details how samples were made and how the preprocessing were done. Please do not add that here.