EricKutschera
commented
8 months ago For a new run, usually it's best to use a new --od and a new --tmp directory (or delete those directories before starting a new run)
rMATS can make use of existing files in --od and --tmp depending on the command line arguments:
- https://github.com/Xinglab/rmats-turbo/tree/v4.2.0#running-prep-and-post-separately
- https://github.com/Xinglab/rmats-turbo/tree/v4.2.0#running-the-statistical-model-separately
The output files in --od would be overwritten by a new run. The .rmats in --tmp have timestamps so new files would not overwrite existing files. The intention is to combine files from multiple runs when using separate prep and post steps. If a rerun uses the same bam files and the same --tmp directory as a previous run then there should be an error: https://github.com/Xinglab/rmats-turbo/blob/v4.2.0/rMATS_pipeline/rmatspipeline/rmatspipeline.pyx#L3684
Hello, I have just started running my scripts and am wondering if i have to clear out my output files or not before rerunning? the temp output i noticed keeps time stamps, however, are the actual output files overwritten or are the results replicated... for example the SE.MATS.JCEC.txt, RI.MATS.JCEC.txt, MXE.MATS.JCEC.txt ... Thanks!