smallRNA profiling using HTSeq error

Question

[abhay.kanodia]

Hello,

I want to create a "count" file using HTseq. I have both BAM file and gtf file:

htseq-count -f bam -s no -i AK1a_clean_Aligned.sortedByCoord.out.bam  gencode.v42.chr_patch_hapl_scaff.annotation.gtf  >> AK1a_counts.txt

It still gives an error:

htseq-count: error: the following arguments are required: featuresfilename

Can someone please tell me why that is? Thanks a lot!

Answer 1

[Buffo]

You're using the -i parameter but is empty, read the manual and specify the attribute you want, or remove it.