search

nloyfer / UXM_deconv

Other
38 stars 12 forks source link

Problem with chromosome names #17

Open fa8sanger opened 2 months ago

fa8sanger commented 2 months ago

Dear Netanel and Tommy,

We have some EMseq data mapped to hs37d5, but ours is a version of hs37d5 without "chr" in the chromosome names. This is giving me problems with uxm. wgbstools bam2pat works without problems and generates the pat.gz files. However, I haven't managed to make uxm work. If I use the downloaded atlases I get Warning: skipping an empty sample, and if I modify the atlas to remove "chr", then I get Invalid atlas: supplemental/Prueba.tsv. "name" column must all start with "chr"

Is this a known imcompatibility and if so is there any trick? or am I just doing something wrong?

Thank you very much for your work, Fede

fa8sanger commented 2 months ago

In case this trick works for others: Instead of trying to make uxm work with non-chr hs37d5, I am modifying myself the pat.gz files so they have "chr":

gunzip XXX.pat.gz
perl -pi -e 's/^/chr/' XXX.pat
bgzip XXX.pat
tabix -C -b 2 XXX.pat.gz
./uxm deconv -o kk.csv XXX.pat.gz

This works for me