Salmon quasi Index upgrade

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4.9 years ago

Morris_Chair ▴ 350

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

RNA-Seq salmon • 1.5k views

ADD COMMENT • link updated 4.9 years ago by Ram 43k • written 4.9 years ago by Morris_Chair ▴ 350

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Re-run indexing with the version of salmon you are using now.

ADD REPLY • link 4.9 years ago by GenoMax 141k

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Most likely the case! Did you recently upgrade Salmon?

ADD REPLY • link 4.9 years ago by Kristoffer Vitting-Seerup ★ 4.0k

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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.

ADD REPLY • link 4.9 years ago by ATpoint 81k

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