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Gene annotations from Ensembl models

See original GitHub issue

I have the Docker image 0.8.7 and versions.txt contains:

SERVER_VERSION: 1.14.2
WEB_APP_VERSION: 1.1.11

I have mcool files that were aligned against cerevisiae R64-1-1. I have a BED file of gene annotations - because it is yeast it has only one exon per gene (see below).

# head /ingest/higlass/annotations/S288C.bed
I	334	649	YAL069W_mRNA	0	+	334	649	0	1	315,	0,
I	537	792	YAL068W-A_mRNA	0	+	537	792	0	1	255,	0,
I	1806	2169	YAL068C_mRNA	0	-	1806	2169	0	1	363,	0,
I	2479	2707	YAL067W-A_mRNA	0	+	2479	2707	0	1	228,	0,
I	7234	9016	YAL067C_mRNA	0	-	7234	9016	0	1	1782,	0,

I have been trying and failing to make this file into a gene annotations track. I have tried to use the guide for adding gene annotations but I couldn’t get that working for the SacCer example (the gzip files wold not extract) but I think some of the steps in that guide a redundant in my case. So I think I can convert the BED file to BEDDB and ingest that into my HiGlass docker container.

I have been going round in circles and just cannot figure out how I can import this data into the container - I have already got the mcool matrices and chromsizes imported and working just great. But this is driving me mad!

Steps to reproduce

clodius aggregate bedfile --chromsizes-filename ../chromsizes-tsv/S288C.chromsizes S288C.bed
python higlass-server/manage.py ingest_tileset --filename /ingest/higlass/annotations/S288C.bed.beddb --coordSystem S288C --coordSystem2 S288C --name 'S288C' --project-name Annotations --filetype beddb

Observed behavior

The track does not get listed in the menu

Expected behavior

I would like to be able to plot the gene models from the attached BED file S288C.bed.txt

Thank you for your time and help

Issue Analytics

State:
Created 2 years ago
Comments:8 (5 by maintainers)

Top GitHub Comments

1reaction

pkerpedjievcommented, Oct 13, 2021

Ah, yes that link is to resgen which uses a slightly different fork of higlass. We need to update higlass to understand the plural datatype as well.

Anyway, glad it works and thanks for asking!

0reactions

ChristopherBarringtoncommented, Oct 13, 2021

That’s got it! Thank you! Not annoying at all!!

I just copied the datatype from the image you shared. But it is now working great.

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