Salmon quasi Index upgrade
Hello everyone,
After running the command line, (it has been a while that I wasn't using salmon and I think something changed),
salmon quant -i gencode_v29_idx/ -l A -r myfile.fq -p 4 --validateMappings --fldMax 150000000 --fldMean 350 --fldSD 250 --numBootstraps 100 --allowOrphans --useVBOpt --seqBias -o myfiles
I get this message red highlighted,
[2019-06-03 14:51:59.275] [jointLog] [critical] I found a quasi-index with version q5, but I require q6. Please re-index the reference.
Can you give an indication about how to proceed for this upgrade?
Do you think I should reanalyze my previous dataset with this new version in order to be consistent?
Thank you
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Ram
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Morris_Chair
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Morris_Chair
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Re-run indexing with the version of salmon you are using now.
Most likely the case! Did you recently upgrade Salmon?
If you plan to analyze the previous samples in the same statistical context I would definitely say yes. Tagging Rob for an expert's opinion.