Help with a reading count command using HTSeq

Question

[flavobacteria]

I am working on bacterial RNAseq data analysis, here is what I have down:

Bowtie:

bowtie -S reference ~/RNAseq/QC/decompressed_mybacteria.fastq > mybacteria.sam

Htseq:

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

[karl.stamm]

You didn't ask a question or say what the problem is.

Answer 1

[Manvendra Singh]

Firstly, I am not sure that this is right command for paired end fastq files , they should be "prefix_1.fastq" and "prefix_2.fastq"

next, I would use featureCount instead of htseq-count, but if you want to use htseq-count, then this is right command.