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-   -   featureCounts output to DESeq2? (http://seqanswers.com/forums/showthread.php?t=85065)

lucyf 10-11-2018 03:48 AM

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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