Hi, I just need to understand the workflow to get the WIG files from bulk RNA-seq. What I know is that we get the raw fastq files, QC, align them to the genome and retrieve the WIG files from BAM files. We do not perform any normalisation since we haven't generated any count data yet. Is my understanding right?
Also, why might some values be negative in the WIG files? I've generated two WIG files from the paired-end sequences: one is forward and one is reverse (I believe since I was generating strand specific files). The negative values are only in the second file (which could be reverse). I'm thinking that maybe something went wrong in the workflow (I used galaxy, so it's automated and shouldn't have but I'm not sure) and I need to re-run it, but could that be the only reason?
Thank you for any help on this!
