rugilemat

Hi, I have been trying to run the installed salmon version on our HPC cluster on minimap aligned ONT reads and got the following error: `processed 0 reads in current...

Issue with talon filter

4

Hi, I have been trying to run talon filter on my database: ```talon_filter_transcripts --db talon/database.db -a Hg38 --maxFracA 0.5 --minCount 1 --minDatasets 3 --o talon/talon_run.csv``` And I'm getting an import...

CPAT3 compatibility

2

Hi there, As far as I understand it's not possible to use CPAT3 with IsoformSwitchAnalyzeR? Are there plans to include this compatibility? I'm struggling to make CPAT2 work and the...

Hi, I've been trying run `swan` as a script on our HPC and it seems that `es_df = sg.find_es_genes(verbose=True)` and `ir_df = sg.find_ir_genes(verbose=True)` take a very long time to run...

**Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?** Salmon **Describe the bug** `419663 Segmentation fault (core dumped) ` **To Reproduce** Steps and data to reproduce...

Eventalign.index from m6anet output and RNA004 compatibility

9

Hi team, I want to compare m6a levels between my samples among other analyses. I first ran m6anet to get sample level m6a output and didn't have the foresight and...

Genome vs transcriptome alignment

4

Hi, I've been trying out m6anet on our RNA004 reads and I have a question about alignment. As a default, we tend to align our reads to the genome for...