lmanchon

Hi, ok it seems to be good for my job. but is there a README file to compile the package ?

ok thank you for your help

-- I think i used the wrong file, i should have taken the 'mosdepth.region.dist.txt' file: python scripts/plot-dist.py -o dist_region.html *.mosdepth.region.dist.txt now the result is closer to plotCoverage output (see attachment)....

-- it seems to be in line 71 ($showlegend) but i don't know how to change this variable.

so nothing obvious for the owl --> obo conversion. it's a problem. The chado schema and the tripal module only recognize the obo format.

it's a problem with all these file formats. there should be a unique standard format, why not the owl. And delete the obo format.

maybe try this computation mentioned here: https://www.biostars.org/p/83842/

problem is over sorry. I forgot to detach stats package and rstatix was masked by stats.

--Hi, if i change from hg38 to gencode in /usr/local/lib/python3.8/dist-packages/cravat/conf/cravat.yml it failed with: Running reporter... Text Reporter (textreporter) Traceback (most recent call last): File "/usr/local/lib/python3.8/dist-packages/cravat/cravat_class.py", line 1619, in run_reporter response_t...

--Hi, i have simulated target-sequencing with paired-reads on targets (chr20.bed) with some CNVs, then when i run cnvkit with: cnvkit.py batch simulated.bam -n -m hybrid -f chr20.fa -t chr20.bed --annotate...