Hi all, I have RNAseq data in fastq format, and I've done alignment with bowtie2, output to SAM, sorted and converted to BAM, then used featureCounts to generate table/matrix of counts for samples.
I've edited the delim file so that it doesn't have the header, or unnecessary columns, but does contain the geneid column, and then subsequent columns for each of my 6 samples (3 of each condition) with counts underneath for each gene.
I want to use DESeq2 to do the differential expression but I'm having a lot of trouble starting out. I can't seem to find anything of how to import the file into DESeq2 to get it to analyse, and all the tutorials I'm finding suggest using salmon, or tximport (which I dont think supports the pipeline I've used..or certainly in the help file, only lists salmon, sailfish, kallisto etc).
Can anyone point me in the right direction of where to find some other info, or give me an idea of where to start? I'm still early in my learning of bioinformatics, and appreciate your support.
You can create a read count matrix using
featureCounts
by feeding it all of your BAM files in the order you want them in the matrix columns (genes will be in rows, samples in columns). You can then read the matrix into DESeq2 using these instructions in DESeq2 vignette.Thanks genomax - will take a look at those instructions