Question: htseq-count output file
1
gravatar for Javad
2.8 years ago by
Javad110
Javad110 wrote:

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

rna-seq • 6.9k views
ADD COMMENTlink modified 2.8 years ago by michael.ante3.6k • written 2.8 years ago by Javad110
5
gravatar for michael.ante
2.8 years ago by
michael.ante3.6k
Austria/Vienna
michael.ante3.6k wrote:

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

ADD COMMENTlink written 2.8 years ago by michael.ante3.6k

Thanks a lot. It was really helpful :)

ADD REPLYlink written 2.8 years ago by Javad110
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