Bioinformatics Forum

RNA-seq pipeline crashed at the end. Do I need to do the mapping step again?

I run the RNA-seq pipeline and it crashed after a day of work.

I see that it already performed the mapping step. Do I need to re-run the entire pipeline or is there a way to skip the mapping step?

Gil Hornung
1 Answer


Whenever a pipeline crashes, the first thing you should do is check the log file (in <run directory>/logs/log.txt). In the log you can see exactly at what stage the pipeline crashed.

When a sample is mapped, its bam file is added to your project repository. If the mapping results exist in the repository, mapping for that sample will be skipped even if you choose to re-run the entire pipeline.

So the answer is - you can either choose "Run All" or "Count" as the starting step. 

Nofar Chen

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