Hi Brandi, I hope you are doing well. I found this script is not able to handle single end reads correctly due to the -p option in the following line. It forces featureCounts to process the bam file as paired end reads. Any thoughts?
https://github.com/medforomics/process_scripts/blob/40acb408857970fddcca1f42354fe226fda5491a/genect_rnaseq/geneabundance.sh#L51C51-L51C51
Hi Brandi, I hope you are doing well. I found this script is not able to handle single end reads correctly due to the
-poption in the following line. It forcesfeatureCountsto process the bam file as paired end reads. Any thoughts?https://github.com/medforomics/process_scripts/blob/40acb408857970fddcca1f42354fe226fda5491a/genect_rnaseq/geneabundance.sh#L51C51-L51C51