Cuffnorm output files gives only geneid and not gene names in annotation
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8.0 years ago
Yaseen Ladak ▴ 30

Hi All,

I need a little help, the output of cuffnorm from the genes.fpkm_table file is as follows:

tracking_id q1_0 q2_0 ECDH10B_0001 0 0 ECDH10B_0002 12.7841 26.1493 ECDH10B_0003 20.8691 21.9675 ECDH10B_0004 25.1604 47.0917

How can I include the gene name in the output file in addition to the gene id which is also present in the input GTF file that I am using from ensembl. I am not discovering any new novel transcripts.

Can any one please help.

Thank you Yaseen

RNA-Seq • 2.5k views
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8.0 years ago
fanli.gcb ▴ 730

Look at the genes.attr_table file

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8.0 years ago
Yaseen Ladak ▴ 30

Thanks but genes.attr_table does not give me the count. I want to have the counts with the gene id and gene names.

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Use the tracking_id to match them up....

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