htseq-count output file

Question

[Javad]

Hi everybody

I am trying to use htseq for counting the number of reads aligned to genomic features. I use the following command:

htseq-count -s no -t exon -i gene_id --additional-attr=gene_name Alignment-files annotation-files

After running the command the read count table is printed on the terminal screen but there is no spreed sheet saved in my current directory. where can I find the output spreadsheet of htseq-count command?

Best

Answer 1

[michael.ante]

Hi Javad,

you need to direct the output to a file :

htseq-count -s no -t exon -i gene_id --additional-attr=gene_name Alignment-files annotation-files > result_file.txt

Cheers,

Michael

[Javad]

Thanks a lot. It was really helpful :)