search

Xinglab / rmats-turbo

Other
217 stars 53 forks source link

Is population data without replication suitable for rMATs? #356

Open qingzengLi opened 7 months ago

qingzengLi commented 7 months ago

Thanks for providing such an excellent tool.I have a question for you I have some RNA-seq data of different genotype materials. They are divided into treatment groups and control groups, but no replication. I want to know whether my data are suitable for rMATs. Thanks a lot!

EricKutschera commented 7 months ago

Yes, that seems fine. It sounds like you have two sample groups, treatment and control, which is what rMATS expects. rMATS checks if there is a significant difference in isoform proportion between the two sample groups given as --b1 and --b2

qingzengLi commented 7 months ago

Wow,Thank you for your prompt reply,The materials in both groups are the same, should I use paired-stats mode?

EricKutschera commented 7 months ago

Here's the README section on the paired stats model: https://github.com/Xinglab/rmats-turbo/tree/v4.2.0#using-the-paired-stats-model

If each input file in the treatment group has a corresponding input file in the control group then you can use --paired-stats. The default statistical model can also be used and it should be much faster. You might try running the default model first to get initial results since --paired-stats could take a while

qingzengLi commented 7 months ago

OK,Thank you for you reply.