addSolexaReads.perl error

wisojo

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Join Date: Jun 2014

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#1

addSolexaReads.perl error

06-20-2014, 08:42 AM

Hey guys,

I'm trying to use the command addSolexaReads.perl to add the rest of my fastq reads to an assembly made with Newbler, but I keep getting the error "-ace must be specified." I think I'm including all of the correct files for the addSolexaReads.perl command but still keep getting that error.

Has anyone come across this before or might know where the problem is coming from?

Thanks!
Tags: addsolexareads, consed, newbler
Danos2000

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Join Date: Nov 2013

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#2

11-10-2015, 10:29 AM

Syntax has changed

The addSolexaReads.perl syntax changed around consed 23.

Old syntax:

Code:

addSolexaReads.perl your_ace_file.ace your_fileoffilenames.fof your_fasta.fasta

New syntax, where you explicitly specify the options:

Code:

addSolexaReads.perl -ace your_ace_file.ace -fastqfof your_fileoffilenames.fof -fasta your_fasta.fasta

More:

Aligning .sff or .fastq Reads to a Reference Sequence Using consed

https://vimeo.com/70137766

This video tutorial demonstrates how to align reads generated by Ion Torrent, 454, or Illumina sequencing to a reference sequence using consed. (Note that the…

--Dan
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