I am working on bacterial RNAseq data analysis, here is what I have down:
bowtie -S reference ~/RNAseq/QC/decompressed_mybacteria.fastq > mybacteria.sam
htseq-count -m intersection-nonempty --stranded=no mybacteria.sam template.gtf > count.sam
My original seq was created by using Hiseq Illumina, paired end.
I know it could be htseq variable I used here is not good.
Anyone can help with this command line? Thank you