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
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