rugilemat

Thanks! I went down CPC2 route as I could get a local CPAT2 version to run. Looking forward to the update though!

Hi, no I'm still trying to work this out.

Hi, I'm sorry it took me so long to get back to you. I had some conflicts with conda environment I was initially trying to run it with. However, it...

Thanks for the quick response! Will look forward to the RNA004 model :) Can I just quickly check if the files were aligned to transcriptome, running `xpore dataprep` with `-genome`...

Hi @yuukiiwa, Thanks so much! Does the `--gtf_or_gff` have to be genomic or is it the transcript gtf?

Hi @yuukiiwa , I think I must be doing something wrong as I can't get `xpore` to work with `--genome` tag. My code is: ``` eventalign="/scratch/prj/ppn_microglia_mod/directrna/xpore/36S_pilot_events.tsv" gtf="/scratch/users/k19022845/refgenome/gencode.v44.primary_assembly.annotation.gtf" ref="/scratch/users/k19022845/refgenome/gencode.v44.transcripts.fa" output="/scratch/prj/ppn_microglia_mod/directrna/xpore/pilot/36S_trial" xpore...

Hi, Thanks for the explanation - I'll give it a go after editing the Gencode annotations. Yes, I've been using `f5c eventalign` for RNA004 as described in `m6anet dataprep` and...

Hi, I'm having the same error. I tried installing via conda environment too but with no luck. They recently updated our HPC system so I think it could be related...

Thanks @yuukiiwa! I did get some output from genome-aligned bams, I'll see if I get to compare them with properly transcriptome-aligned files but I will stick to transcriptome-alignments for my...

Hi @yuukiiwa, Thanks so much! If I'm interested in read-level modifications from the documentation I understand that higher `--num_iterations` is recommended while `--num_iterations 5` should be sufficient for site-level analysis?