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Old 10-11-2018, 03:48 AM   #1
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Location: UK

Join Date: Oct 2018
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Post featureCounts output to DESeq2?

I am doing an RNA-seq analysis where I have used featureCounts to count the number of reads per gene feature. The output looks like this:

Geneid Chr Start End Strand Length sample.sorted.bam
gene:CDR20291_3551 Chromosome 9450 9857 + 408 5
gene:CDR20291_3552 Chromosome 9857 10630 + 774 53
gene:EBG00000018530 Chromosome 10716 12345 + 1630 4

Will DESeq2 understand this table? If not, how do I trim this to contain only the gene id from the first column and the counts from the last column?

Thanks in advance!
lucyf is offline   Reply With Quote

alignment, deseq2, featurecounts, gtf, rna-seq

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