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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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Which sequence search engine do you recommend for best comparison with your curated GTF files? #203

Closed jacel closed 1 month ago

jacel commented 1 month ago

Hi, I am trying to look at repeat elements in different strains of mice. I am planning to run repeatmasker on the new long-read SPRET genome, and compare these results with your mm10 GTF. So I want to use the same sequence search engine you used, to ensure they are comparable. Do you recommend Cross_Match, RMBlast, HMMER, or ABBlast? And are there any other RepeatMasker options you recommend using? Thank you!

olivertam commented 1 month ago

Hi,

Thank you for your question. We used the UCSC RepeatMasker track, so following their approach would be best.

Thanks.

jacel commented 1 month ago

Ah UCSC has already run RepeatMasker on Spret so I will use this file. Thank you!