PSI value per sample

[Alex PG]

Hi Biociphers community,

I was wondering if it’s possible to export the PSI values for each individual sample as visualised in Viola View.

In the modularized TSV files I’ve checked so far, I’ve only been able to find the median PSI values for groups, rather than per-sample values.

All the best,

Alex 

[San Jewell]

Hi Alex, 

There was an experimental feature for this developed for a one off use case in modulize/tsv, --show-per-sample-psi switch, but it's only for heterogen runs at the moment. I can check into expanding it to other cases in our next update since this is something you find useful. In the meantime it is possible to open the zarr PsiCoverage files to extract the psi directly per sample, likely with this function: https://biociphers.bitbucket.io/majiq-docs/generated/rna_majiq.PsiCoverage.bootstrap_psi_mean.html  ; I can help you get started with the api as well if you are interested in it. 

Also, in general, values shown in voila are median over reads in the splicegraph, and mean over psi values per sample/group in the lsv rows. 

Thanks, 

-San

[Alex PG]

Hi San,

Thank you so much for your answer and huge apologies for the late reply! I reran with the --show-per-sample-psi switch and it worked! This is exactly what I wanted. Really appreciate your help!

All the best,

Alex

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[San Jewell]

Yay! Please don't hesitate to reach out if you have any additional questions. 

-San