newest human and mice genome annotations

[gvcaldas]

Hi, I have not been able to create a new annotation file in higlass, using the latest human annotation (gencode.v42.primary_assembly.annotation.gtf). The human gene annotation on the higlass server is not the newest. The Refseq file from UCSC, necessary to create the newest annotation in higlass, does not exist (also outdated). We did chat on slack about this issue before and we tried the script you suggested (which uses a GFF3 file to generate: i. Chromosome sizes file and ii. Bed file - which is used to generate the final gene annotation file for higlass). However, The new scripts do not take into account all the possible annotations and conditions in the GFF file which result in multiple entries per chromosome in the chrom.sizes file as well as for a chromosome labelled as “Unknown”.
The unknown chromosome entries are being added due to the annotations in the GFF file provided by NCBI. If we use these set of files to generate the gene-annotation file, the generation is successful but higlass doesn’t load the file and errors out due to multiple entries per chromosome.

We don't know how to fix this. Do you have suggestions? - or any chance you can add the latest human genome annotations on the server? -
same situation with the mouse genome. mm10 is the latest and not m39. Although, I have not tried yet creating the latter (not sure if the refseq is updated in UCSC).
Thanks!

PS: I lost my access to slack_higlass with my previous email. Any chance I can be added back with gvcaldas@gmail.com?

[nvictus]

The current invite link shouldn't have restrictions, but I sent one to your email anyway.