Sowmya Parthiban

Results 15 comments of Sowmya Parthiban

Interpreting warning messages in discovery only mode

Hi Andre, Thank you for your quick and detailed response. I believe this is because I ran minimap2 without setting the splice aware parameter. Will update this thread after rerunning...

No error model errors when using --ont option

hi @callumparr, I'm running into something similar, just wondering if you have a better idea now on your last comment (as in what qualifies as many errors)? thanks.

question on multisampling

``` library(bambu) library(BiocFileCache) library(readr) library(sessioninfo) library(dplyr) # gtf.file

question on multisampling

thank you, Andre!

question on multisampling

Suppose I split the samples by chromosome, and generated read classes for these separately, can I put these chromosome_wise_ read class files together before generating the extended annotation?

question on multisampling

I was able to save my extended annotation to a gtf for `quant = FALSE` and `discovery = TRUE`. This is what it looks like when I load it. ```...

analyzePFAM error with isoquant data

Hi, are there any updates on this? thanks!

Add Progressive Reinforcement Capabilities (potentially via Q-Learning)

I am interested in this issue. @javierhow is willing to help.

trying to understand the `OUT.novel_vs_known.SQANTI-like.tsv`

Pasting a few lines from the file here. ``` transcript372.chr1.nnic chr1 + 2357 11 novel_not_in_catalog ENSG00000187634.13 ENST00000341065.8 2191 12 76 1 76 0 alternative_structure_novel;correct_polya_site_right FALSE True NA NA NA NA...

read assignment information

Hi Andre, thank you for super quick response, My bam file contains the read IDs, so I don't think that's the issue. This is what my metadata looks like for...