Jiang Hao

> Thanks for your support, for `geneset_enrichment` we need to modify two parameters, one for `background` and the other for `pathway_dict ` if it is not a model organism: >...

> This looks like a disk I/O problem. Is there a chance your run IsoQuant on some network disk, e.g. NFS share? > > Best Andrey thank you! i don't...

> I guess it can. IsoQuant uses gffutils, which creates and SQL database from the gene annotation on disk. Unfortunately, it is not possible to create a database connection on...

> I guess it can. IsoQuant uses gffutils, which creates and SQL database from the gene annotation on disk. Unfortunately, it is not possible to create a database connection on...

Thank you for your patient reply! But I still have some questions. > You may also be interested in the entropy [command](https://nanoporetech.github.io/modkit/intro_entropy.html). You could calculate the entropy on each transcript...

Hello, @tamalarafat . Thans for your helpful reply ! I am glad to konw more details about your pipeline!

Hello, @tamalarafat Thanks for sharing!

> dorado basecaller > -x cpu > --modified-bases m6A > --mm2-preset splice -k14 > --no-trim > /lustre/home/jianghao/workspace/01.RNA-seq/DM_bulk_ONT/output/dorado/[email protected]/ > /lustre/home/jianghao/database/05_RNA/01_DM_ONT/pod5/LDL-1/pod5_pass_1/ > LDL-1.bam Thank u! But some problem still ``` [2024-08-06 09:21:10.563]...

> Can you add verbose logging with `-vv` please? yes, I add -vv. But a new error occurred. `Error code 12 (Cannot allocate memory)`. Would setting higher RAM help? How...

> Yes - It looks like you're running out of memory. > > Also this **isn't the same command** you were having issues with as it doesn't contain the `--modified-bases`...