search

mhammell-laboratory / TEtranscripts

A package for including transposable elements in differential enrichment analysis of sequencing datasets.
http://hammelllab.labsites.cshl.edu/software/#TEtranscripts
GNU General Public License v3.0
217 stars 29 forks source link

T2T_refGene.gtf & T2T_rmsk_TE.gtf #126

Closed heeralvi closed 1 year ago

heeralvi commented 1 year ago

Hi Team,

Thanks for developing this wonderful tool, i am working RNA seq data using T2T as a reference (https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/analysis_set/chm13v2.0.fa.gz). I have been trying to make gene reference and repeat masker file but i am getting an error in gtf format. I was wondering if you can help me to get these reference file, that would be very helpful.

Thanks

olivertam commented 1 year ago

Hi,

You can try to get the RefSeq gene annotations (as GTF) from UCSC Table Browser. I think it should work without any modifications (just make sure the chromosome names matches your FASTA file (i.e. your FASTA file starts with "chr")). For the TE annotation, you can download the GTF here. Let us know if you are still encountering issues.

Thanks

heeralvi commented 1 year ago

Hi Oliver,

That was very helpful, solved the problem, Thanks a lot.

github-actions[bot] commented 1 year ago

This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 5 days