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Old 02-01-2018, 11:44 AM   #1
gacarson
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Location: Stanford, CA

Join Date: Feb 2018
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Default Picard tools - CreateSequenceDictionary

Hi there,

My goal is to use picard tools to estimate % on target rates for a recent target enrichment experiment we performed. Collecthsmetrics seems like a good tool for the job, and so I installed picard to use at the command line. That tool requires that I use the BedtoInterval command, which needs a .dict file from CreateSequenceDictionary. I downloaded my reference fasta file, but am struggling to get CreateSequenceDictionary to run.

Usage example:

java -jar picard.jar CreateSequenceDictionary \
R=reference.fasta \
O=reference.dict

My attempt:
'''gacarson$ java -jar picard.jar CreateSequenceDictionary \ reference.fasta'''
ERROR: Invalid argument ' reference.fasta'.

I've also tried putting 'R=' in front of my file name with no luck.

Any suggestions on how to get this working?

Thanks for the help.

Cheers,

-Glenn
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Old 02-01-2018, 11:49 AM   #2
gacarson
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Location: Stanford, CA

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Default

solved! It was that \ that was killing it. I thought that \ was needed in the code.

'''java -jar picard.jar CreateSequenceDictionary R=reference.fasta''' worked!

feel free to delete the thread, or leave it so it's searchable
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Old 02-01-2018, 12:36 PM   #3
seb567
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Location: Québec, Canada

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Posts: 258
Default

Thanks for posting the solution.
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