mm39 genePred file

Question

[christoph.neu]

Hello,

i need a gene annotation file for the mm39 mouse genome in the genePred format. I found that there is a utility which can convert the information from the gtf format. However, where I would download the gtf file it says that it was created by a conversion from the genePred format.

Of course I could still reconvert it to genePred, however this seems wrong. Is there an official source for the genePred format where I can directly download it from?

Answer 1

[vkkodali_ncbi]

Assuming that you are interested in RefSeq annotations, you have the following options:

1. Use UCSC Table Browser and download the table. You can use the settings shown in the screenshot below. More information about the data included in this track can be found here. In particular, note that there is an additional bin column that you may have to remove before downstream processing.
2. Download RefSeq annotation in GFF3 format from NCBI and use the UCSC utility gff3ToGenePred to generate the GenePred file:

   $ wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/10090/109/GCF_000001635.27_GRCm39/GCF_000001635.27_GRCm39_genomic.gff.gz
   $ zcat GCF_000001635.27_GRCm39_genomic.gff.gz | gff3ToGenePred -refseqHacks stdin mouse.genepred
   

[christoph.neu]

thanks a lot. The bin column was actually something I needed so the conversion with gff3ToGenePred or gtfToGenePred did not create the exact format required downstream.