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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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Gene ordering file #464

Open sararosengithub opened 1 year ago

sararosengithub commented 1 year ago

The instructions to make a Gene ordering file is unclear. can you please add a few words about the files needed : your_reference.gtf and your_gen_pos.txt Thanks

GeorgescuC commented 1 year ago

Hi @sararosengithub ,

There is information about the gene position file on the wiki as well as a link to download some of the most common ones.

The reference gtf file is only needed if you do not already have a gene positions file as detailed above. You can use any file in the gtf file format that contains the gene information for the reference genome you want to use and process it using the scripts/gtf_to_position_file.py script. You may however need to filter it to remove pseudogenes or duplicate names.

Regards, Christophe.