count reads per gene

1

I would like to count my human sample RNAseq data transcript using the BAM file. I had converted the file to BAM and now I am unable to generate the read counts per gene. The steps that i followed were
click on sam/bam to count matric using HTseq–>only changes that i made is transcript. I have attached the screenshot of the

Screen Shot 2020-07-27 at 5.20.48 PM
Screen Shot 2020-07-27 at 5.20.48 PM1440×900 322 KB
trouble that I am getting. syntax error
illegal strand

Please help

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2

Hi,
This error can arise if you selected the option Stranded:yes with non stranded data. If that is the case you can try rerunning the task with the option Stranded:no.

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Hello, I have the same problem, and also did the change that DELPHINEL suggest, but didn’t work… it keeps showing the same error.

Could you tell me if you could fix it? :slight_smile: