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TobyBaril / EarlGrey

Earl Grey: A fully automated TE curation and annotation pipeline
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annotations in gff file not shown in IGV #111

Closed ting-hsuan-chen closed 3 months ago

ting-hsuan-chen commented 4 months ago

Hi Toby,

I tried to upload the GFF file generated by EarlGrey to IGV but found many TE annotations existed in the GFF file were not shown in IGV. The BED file doesn't have this problem.

The following image is a screenshot of IGV over 562kb. The first track is the GFF file and the second track is the BED file. You can see many TE annotations presented in BED file were not shown in the GFF track. The IGV version is Version 2.13.2.

IGV_EarlGrey_gff

The following screenshot of the GFF file showed 10 TE annotations, but only the 3rd and the 10th were shown in IGV (see the following image). image

image

I couldn't figure out what's causing this. The same problem was observed in GFF files generated by EarlGrey in other genomes. Any guidance to solving this problem would be much appreciated.

Best wishes, Ting-Hsuan

TobyBaril commented 3 months ago

Hi Ting-Hsuan!

Hmm, this is very odd. I'm not overly familiar with IGV, but it should be able to parse the GFF without any issues, which it seems to be doing for at least some of the TE annotations. The normal things I would check are carriage return format at the end of the line, that the fields are correctly tab separated etc. None of this should have changed if the files haven't been opened in any other softwares.

I would recommend asking in the IGV help group here: https://groups.google.com/g/igv-help/ . They are likely to be able to provide a better answer than I can,

Best wishes,

Toby

SwiftSeal commented 3 months ago

I also just happened to notice this, using v2.17.4. This does not seem to be the case for the web viewer however? Sounds like an IGV issue 🤷

TobyBaril commented 3 months ago

closing for the moment as linked to a separate software