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jpuritz / dDocent

a bash pipeline for RAD sequencing
ddocent.com
MIT License
52 stars 41 forks source link

"rename.for.dDocent" not working #3

Closed ghost closed 9 years ago

ghost commented 9 years ago

Hi.

I'm pretty new to genomics and using the command line, but I was wondering if this is an easy fix:

~/Documents/ddocent-master$ ls bars.names install_dDocent.FB_requirements README.md bars.names~ install_dDocent.GATK_requirements rename.for.dDocent dDocent.FB LICENSE Rename_for_dDocent.sh dDocent.GATK mergefq.pl

~/Documents/ddocent-master$ sh rename.for.dDocent bars.names rename.for.dDocent: 9: rename.for.dDocent: Syntax error: "(" unexpected (expecting "fi")

Can't seem to get barcode file to work - instructions followed exactly as on the blog. As far as I am aware I have the newest version of dDocent.

Also, are there sample data sets to available for dDocent?

Cheers,

~ jat101

jpuritz commented 9 years ago

The script requires that you have files that were demultiplexed via process_radtags from Stacks and also that files are gzip compressed. Tutorials and data sets will be posted in the next few days.