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kcleal / gw

Genome browser and variant annotation
MIT License
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Display IDs instead of gene names when loading .gff3 and .gtf files #43

Closed villena-francis closed 3 months ago

villena-francis commented 3 months ago

Hi @kcleal!

First of all, I don't quite know if what I am commenting on is really an error or if I am asking for the implementation of a new functionality... Thank you (again) in advance for your effort and help.

From an Intel PC with Ubuntu 22.04, when I load .gff3 or .gtf files to see the gene names under my reads, what GW shows from both files are the values from the "gene_id" column instead of the "gene_name" column. Therefore, what is displayed on the screen are alphanumeric identifiers like "ENSG00000141510" instead of "TP53". Would it be possible to make some adjustment to change that behavior? It's already hard enough to remember the names of the genes one works with, if now they also need to be recognized by IDs with more than 12 digits...... :'-(

Captura desde 2024-07-29 19-06-48

kcleal commented 3 months ago

Hi @villena-francis, v1.0.1 has been released and should hopefully show the correct information. Let me know if still needs work.

villena-francis commented 3 months ago

Hello again!

Well, I have some good news and some bad news:

In the following image, the annotation at the bottom corresponds to gft, and the one above to gff3.

Captura desde 2024-07-31 22-42-17

kcleal commented 3 months ago

Ok, sorry about that. Was the gff3 file also indexed? It looks like the gtf rendering could also do with some more work, there seems to be some confusing lines and overlapping blocks being drawn.

villena-francis commented 3 months ago

The only thing I did was download the GFF3 from the GENCODE website, unzip it, and drop it into the GW window (I didn't even know they could/should be indexed...).

kcleal commented 3 months ago

You can index using bgzip and tabix, should get rid of the initial loading time.

I will get this fixed early next week.

kcleal commented 3 months ago

Hi @villena-francis, I think the v1.0.2 fixes this issue. GTF/GFF3 drawing should also be a bit cleaner

villena-francis commented 3 months ago

Hi @kcleal!

I notice this new version of the deb package is smoother, especially when loading and viewing BAM files. Regarding the specific issue, the GFF3 files load correctly.

Thank you very much for your efforts, your tool will be very useful for my master thesis.