Salmon Script Troubleshooting for RNA Seq Data
Hello!
I am working on a Slurm sbatch bash script to perform RNAseq analysis with Salmon in an HPC environment.
I keep receiving the error "salmon quant was invoked improperly" but can't figure out where my error is.
Can anyone spot any errors to help me figure this out?
Script and slurm.out error are attached.
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ATpoint
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makylakb •
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makylakb •
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Make sure the index was created properly. Similar issue has been discussed in the following thread.
https://github.com/COMBINE-lab/salmon/issues/197
mates2value is being concatenated at the end ofmates1. It is not immediately apparent as to why that is happening. That is leaving values ofmates2blank. Check the values offq1andfq2and make sure they are coming through properly.Pdac_Barhee...._normalized_index. You should add that name at the end of the long string for the salmon index.