Numreads from samtools for Differential Expression
1
0
Entering edit mode
16 days ago
pedroc.c • 0

Recently I've been wondering if the numreads from samtools coverage could be used as count tables for posterior differential expression analysis (DESEQ2, EdgeR), the results would be different from using counts from FeatureCounts?

samtools featurecounts rna-seq deseq numreads • 288 views
ADD COMMENT
2
Entering edit mode
16 days ago
GenoMax 146k

If you are going to go through the trouble of defining regions corresponding to each exon and then adding those counts up (when using samtools coverage), why not stick with featureCounts that understands splicing and will make use of the gene models in the GTF file. samtools coverage would also not know about multi-mapped reads which need to be properly addressed during counting.

the results would be different from using counts from FeatureCounts?

Yes results would be different and perhaps not logical (unless you are dealing with non-overlapping non-spliced genes with no multi-mapped reads).

Use correct tool meant for a specific analysis. Because samtools overage is going to give you counts they are not necessarily going to be usable as is for DE analysis.

ADD COMMENT
1
Entering edit mode

I agree that samtools coverage is not a standard tol for such task. Use featureCounts as suggested. It is fast and efficient, plus simple to use.

ADD REPLY

Login before adding your answer.

Traffic: 1205 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6