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mhammell-laboratory / TElocal

A package for quantifying transposable elements at a locus level for RNAseq datasets.
GNU General Public License v3.0
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locInd file for GRCh37 #15

Closed kiekyon closed 2 years ago

kiekyon commented 2 years ago

Hi,

Can I check if you have a pre-built locInd index for GRCh37?

Thanks

KK

olivertam commented 2 years ago

Hi,

Are you using the GRCh37 genome FASTA from Ensembl (canonical chromosomes are just numbers, e.g. 1), or is it from GENCODE (canonical chromosomes have chr in front, e.g. chr1)? We don't have it currently, but we can start making it.

Thanks

kiekyon commented 2 years ago

Hi Oliver, thanks for the kind offer.

I am using the Ensembl version.

olivertam commented 2 years ago

Great. We are building index now, and will get back to you when it's done. It might take a couple of days.

Thanks.

olivertam commented 2 years ago

Hi, Sorry for my slow response. The index for GRCh37 Ensembl is here. Please let me know if you encounter any issues.

Thanks.

kiekyon commented 2 years ago

Thanks a lot. The index work well.

KK