Error with DESeq2 "all samples have 0 counts for all genes"


I have run a microRNA analysis using BWA and HISAT2 as mapping tools and with both I used HTSeq-count and then tried using DESeq2. With both different runs (for the different aligners) I have gotten the same error multiple times and I am not sure why. (I used the UCSC genome browser microRNA database for both). I have also ran other aligners and have gotten DESeq2 to work so I am just confused. The HTSeq count has 2,315 lines of data so I am no sure why DESeq2 states that there are no counts.

This is the error code:

Fatal error: An undefined error occurred, please check your input carefully and contact your administrator.
Error in DESeqDataSet(se, design = design, ignoreRank) :
all samples have 0 counts for all genes. check the counting script.
Calls: get_deseq_dataset … DESeqDataSetFromHTSeqCount -> DESeqDataSetFromMatrix -> DESeqDataSet

Thank you!

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Take a look at this post. It might help.

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