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

Code should be placed in three backticks as shown below


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

sessionInfo( )

DESeq2 microRNA HTSeq • 1.3k views

ADD COMMENT • link 2.0 years ago • updated 24 months ago abhay.kanodia • 0

score 1 · Answer 1 · 2022-12-24

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ATpoint ★ 4.6k

@atpoint-13662

Last seen 1 day 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 2.0 years 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 2.0 years 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 2.0 years 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 2.0 years 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.