htseq-count no result give me

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4.9 years ago

yaghoub.amraei ▴ 10

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 • 1.2k views

ADD COMMENT • link updated 4.9 years ago by Ram 43k • written 4.9 years ago by yaghoub.amraei ▴ 10

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No results meaning blank file or no features?

ADD REPLY • link 4.9 years ago by Asaf 10k

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No results meaning blank file

ADD REPLY • link 4.9 years ago by yaghoub.amraei ▴ 10

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

ADD REPLY • link 4.9 years ago by Asaf 10k

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ADD REPLY • link 4.9 years ago by yaghoub.amraei ▴ 10

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

Not a link... Post some lines.

ADD REPLY • link 4.9 years ago by WouterDeCoster 47k

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

ADD REPLY • link 4.9 years ago by GenoMax 141k

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