Question: htseq-count no result give me
0
gravatar for yaghoub.amraei
17 months ago by
yaghoub.amraei10 wrote:

hi all

i have work with htseq-count. but no give output for me.

yghb@yghb-virtual-machine:~/amraei/count$ htseq-count -f bam ~/amraei/bam-file/A1.bam ~/amraei/gene/Zea_mays.B73_RefGen_v4.42.gtf > A1-count.txt
rna-seq • 359 views
ADD COMMENTlink modified 17 months ago by RamRS30k • written 17 months ago by yaghoub.amraei10

No results meaning blank file or no features?

ADD REPLYlink written 17 months ago by Asaf8.4k

No results meaning blank file

ADD REPLYlink written 17 months ago by yaghoub.amraei10

Any error messages? Can you post some lines from the gtf file and the bam file?

ADD REPLYlink written 17 months ago by Asaf8.4k

enter link description here

ADD REPLYlink written 17 months ago by yaghoub.amraei10

Can you post some lines from the gtf file and the bam file?

Not a link... Post some lines.

ADD REPLYlink written 16 months ago by WouterDeCoster44k

Do chromosome identifiers in your gtf and alignment files match? That would be the first thing to check.

ADD REPLYlink written 17 months ago by genomax90k
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