I am trying to compare the data from 2 sequencing machines. I aligned my data with Kallisto and then I performed DESeq2 like I normally do. I was checking to see if I was getting similar results from DESeq2. There was a number of genes that had a padj<0.05 in one of the machines but not the other. I was asked to check the gene properties (eg GC, repetitiveness, average expression level) of those genes.
For the average expression level I plotted a scatter plot of the average counts from DESeq2 for each group. I am not sure how to check for GC or repetitiveness. Is that something that I could check on IGV? For the record I have more than 100 genes to check.
You can use geecee in Linux with a BAM file as input to check GC content of your genes.
Do you know if I can use geecee with kallisto genomebam files?
I don't know, but I would think so. It's worth a try.