Darek Kedra

Hello, Sorry for the delay. I have found some non-intuitive output of d4tools and pyd4, see below. In short: how comes that the mean coverage value for 100bp interval is...

Hello, In case it is needed I can share the d4 file/minimal example giving that result. Or a mini-bam file. * d4_tools version: D4 Utilities Program 0.3.4 * installed: ```conda...

Hi Vitor, I need to go through the old notes/emails to check the steps. I will keep you posted. Darek

Hello Vitor, I have not found the working solution. But maybe we can figure it out. The ubu bed format is BED12 one line per transcript: ``` chr1 11873 14409...

For reading fasta either as a random access or probably also in parallel having a fasta index (.fai) makes a huge difference. Packages like pyfaidx compute such index when dealing...

Thank you very much for such a quick answer. Bit of a follow up: the resulting .adam files are in a parquet format readable by say arrow?

Hello, I can confirm that so far I have no issues reading parquet files created by ADAM using python polars. The only a bit confusing thing was with a test...

@tim-rex Instead of ```pigz some_glob_pattern" you may try using a loop: ``` for fn in some_glob_pattern do pigz $fn done ``` Hope it helps, DK

Dear Sebastian, Thank you for your sed oneliner. I ended up writing a small Python script going through all result.stk files and putting the corresponding ID lines. So in that...