Hello,
I am trying to get normalised gene counts for one biological replicate. I got the sequencing done by novogene and they have bam files. They said they use edgeR for normalising one replicate but I can’t get edgeR to work for me. Does anyone know how to use edgeR or what other options there are for normalising one rep? Many thanks
Hi @rbriggs98
I believe edgeR cannot handle BAM files. It works with count tables, and it can produce normalized read counts table(s) as an additional output. If yoou have other replicates, get count tables for every replicate and find differential expression using edgeR. Activate additional outouts for edgeR job (normalized counts).
Hope that helps.
Kind regards,
Igor