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ren-lab / deltaSVM

Codes to run deltaSVM models to predict allelic TF binding
GNU General Public License v3.0
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hg38 reference genome? #5

Closed RegnerM2015 closed 3 years ago

RegnerM2015 commented 3 years ago

Hi @yjqiu

Does deltaSVM work with the hg38 reference? Will the models be transferable?

Thanks!

RegnerM2015 commented 3 years ago

Just figured this one out! From the README:

Other genome builds can also be used, but you need to make sure the SNP file and fasta file are from the same genome build. Also, you need to change hg19.fa in the run.sh to corresponding files.

TaoHJiang commented 2 years ago

Hi @yjqiu

Does deltaSVM work with reference sequences for other species? Thanks!

yjqiu commented 2 years ago

@TaoHJiang I don't think so because the SELEX data is generated for human TFs and TFs from difference species may not share the same sequence specificities.