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ningbioinfo / FeatureCount2GCT

This is a script to convert the output from FeatureCount to GCT format expression tables
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Add meaningul description info #2

Open jimmybgammyknee opened 6 years ago

jimmybgammyknee commented 6 years ago

Can some meaningful annotation be added to the description field? Perhaps being able to download the gene information (HUGO gene name or function) from biomart using the gene names in the first field?

ningbioinfo commented 6 years ago

But the gct file format is pretty strict, it requires only 2 lines of description (the version line, and the row&col count line), because the following script used in the gtex pipeline is line-dependent(quite lazy). And the gene name in the outcome is depend on the the gene name used in feature count

jimmybgammyknee commented 6 years ago

Ah so its only for genome coordinates? I thought i saw an example which had functional information in that field...

jimmybgammyknee commented 6 years ago

Example on the site: https://software.broadinstitute.org/software/igv/sites/cancerinformatics.org.igv/files/linked_files/example.gct

ningbioinfo commented 6 years ago

Right, you mean the second column, I thought you mean the metadata like in the vcf files. I'll check biomart to see if I can make a dictionary obj to add that.

jimmybgammyknee commented 6 years ago

Maybe this? https://github.com/daler/biomartpy