cellgeni/bulk_rnaseq

Wrapper scripts for convenient processing of bulk RNA-seq experiments

bulk_rnaseq's Issues

star_bulk.sh

Dear cellgeni IT,

I would like to let you know a couple of things that I had to modify in order to being able to run the star_bulk.sh

1. I had to add to being able to run it: module load singularity

(I also added module load star, I don't know if this one was necessary, but just in case)

2. line 131: $CMD samtools view -@$CPUS -F8 -d NH:1 -O BAM Aligned.sortedByCoord.out.bam | samtools sort -@$CPUS -n -O BAM - > Uniq_paired_namesorted.bam
   I had to modify as follow (adding $CMD):
   $CMD samtools view -@$CPUS -F8 -d NH:1 -O BAM Aligned.sortedByCoord.out.bam | $CMD samtools sort -@$CPUS -n -O BAM - > Uniq_paired_namesorted.bam

I think those are all the things I needed to modify to make it run.

Thank you, have a nice week!!