Question: htseq-count no result give me
0
gravatar for yaghoub.amraei
6 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 • 232 views
ADD COMMENTlink modified 6 months ago by RamRS24k • written 6 months ago by yaghoub.amraei10

No results meaning blank file or no features?

ADD REPLYlink written 6 months ago by Asaf6.5k

No results meaning blank file

ADD REPLYlink written 6 months ago by yaghoub.amraei10

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

ADD REPLYlink written 6 months ago by Asaf6.5k

enter link description here

ADD REPLYlink written 6 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 6 months ago by WouterDeCoster42k

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

ADD REPLYlink written 6 months ago by genomax74k
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