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Old 10-11-2018, 04:48 AM   #1
lucyf
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Location: UK

Join Date: Oct 2018
Posts: 2
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!
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alignment, deseq2, featurecounts, gtf, rna-seq

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