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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
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TE annotation for Rabbit (oryCun2) #174

Closed hiskobay closed 3 months ago

hiskobay commented 5 months ago

Hi team, I am utilizing TEtranscripts (and TEcount), and it works well for both human and mouse datasets. Now, I am looking to apply it to Rabbit RNA-seq datasets. However, a TE_GTF file specific to rabbits (e.g., oryCun2) is not available in your web storage. Could you please guide me on how to prepare the GTF file for rabbits? Thank you.

olivertam commented 5 months ago

Hi,

Thank you for your interest in the software. If you are using sequences obtained from UCSC (e.g. oryCun2), you should access the Table Browser and obtain the UCSC rmsk table. You can then use our perl script to generate the TE GTF file as follows:

$ perl makeTEgtf.pl -c 6 -s 7 -e 8 -o 10 -t 11 -f 13 -C 12 -S 2 -n UCSC_rmsk [RMSK table] > [TE GTF]

We have generated a version of the oryCun2 TE GTF that you can try to see if it works.

Thanks.

github-actions[bot] commented 4 months ago

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hiskobay commented 4 months ago

Sorry for my late reply. The TEcount worked well with the rabbit GTF file you provided. Thanks!