no change in input and output of htseq readcount

Question

[KMS]

Dear All,

I am performing htseq read count from GTF and SAM file in ubuntu 22.04, command is running properly but there is no change in given input and output files generated. I open both visibly there is no change when open both files in notepad.

Please guide me.

Thanks

[Ram]

You used NA as a tag, which makes no sense. Please use relevant tags that are helpful as subject matter information. I've changed the tags - removed the NA and added a more relevant htseq tag.

[KMS]

Thanks for correction I am very new user on Biostar community. I am analyzing bacterial RNASeq data for which I used bowtie2 for alignment and obtained results in the form of SAM which I converted in BAM and sorted BAM files. Further I used Subread feature count for gene count from BAM but not succeeded and obtained Successfully assigned alignment (0.00%) after multiple efforts (I also posted a question about it).

After that I tried ht-seq and used SAM and GTF file to get gene count matrix, one input SAM file (2.1 GB) processed and took 20-30 minute to process and obtained results in the form of outcount.txt. but of same size (2.1GB) file when I open input and output file header and everything was same. there was no column or tab data of gene/read count (exactly same as input).

htseq count -o outcount SAM GTF

Kindly suggest. Thanks

[Ram]

I am not familiar with htseq but with the tag added in, people with expertise in htseq should find your post and be able to help you.