batch correction inbetween prep and post step

[Lydia Herzel]

Hi,

I am using rMATS 4.1.2 to get significant alternative splicing events for dozens of knock-down RNA-seq samples that have been prepared in replicates, but in different batches. Hence, I decided to roughly follow the methods of this publication (https://www.nature.com/articles/s41586-020-2077-3, screenshot attached). I know this was discussed in an older post, but some aspects remain unclear to me....  

Could you explain the file structure of the .rmats files to me that I can make the necessary adjustments?

Thanks!

Lydia

[kutsc...@gmail.com]

Here's the related github issue: https://github.com/Xinglab/rmats-turbo/issues/111

I don't think you want to use the .rmats files, but here's the code that parses the .rmats files: https://github.com/Xinglab/rmats-turbo/blob/v4.1.2/rMATS_pipeline/rmatspipeline/rmatspipeline.pyx#L3534

The screenshot says that "the inclusion junction counts and skipping junction counts of all samples were collected from rMATS temporary files". You can get those counts from the final output files like SE.MATS.JC.txt in the columns like IJC_SAMPLE_1. Those counts are also in the files like JC.raw.input.SE.txt. If you want to do some normalization on the counts you could edit those files and then follow https://github.com/Xinglab/rmats-turbo/tree/v4.1.2#running-the-statistical-model-separately to run the statistical test on the modified files

Eric