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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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Question about the hg19_rmsk.vcf file #78

Closed xunchen85 closed 3 years ago

xunchen85 commented 3 years ago

Hi,

I have used the hg19_rmsk.vcf file for some analyses. I am trying to find the original repeatmasker alignment output file. I am wondering where I can find it?

I have tried the repeatmasker human reference database http://www.repeatmasker.org/species/hg.html. There are many versions of hg19, although none of them exactly matched the one I obtained from the TEtranscripts webpage.

Thanks for your help, Xun

olivertam commented 3 years ago

Hi,

We are using the RepeatMasker output provided by UCSC, specifically the rmsk table (downloadable here). We then process the rmsk table with a custom Perl script to generate the GTF file that we provided on our webpage. Please let us know if you have further questions.

Thanks.

xunchen85 commented 3 years ago

Hi,

Thanks very much for your quick response.

I will check if i can find any information from UCSC pointint me to the original repeat alignment results.

Best, Xun