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Old 11-10-2011, 10:52 PM   #1
prettyPeas
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Location: Berkeley, CA

Join Date: Jun 2011
Posts: 1
Default Error in cdna for newMapping

I followed the following directions for aligning 454 reads to an assembled rna-seq dataset.
newMapping projdir
addRun [options: -p, -lib, -mcf] [projdir] filedesc
removeRun [projdir] filedesc
setRef [options: -gref, -cref, -random] [projdir] refdesc
runProject [options] [projdir]

I got the following error when I tried to use the -cref option with setRef
my command:
setRef -cref DH1 /fullpathname/grossSilber.fa
error:
Error: File is not a fasta file of sequence: -cref

Is there a particular format for a cref fasta?

It worked when I setRef with no options, but of course runProject won't work with -cdna

Any helpful hints?
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Old 11-14-2011, 01:12 AM   #2
flxlex
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Location: Oslo, Norway

Join Date: Nov 2008
Posts: 415
Default

Quote:
Originally Posted by prettyPeas View Post
I got the following error when I tried to use the -cref option with setRef
my command:
setRef -cref DH1 /fullpathname/grossSilber.fa
error:
Error: File is not a fasta file of sequence: -cref
I am pretty sure the problem is the 'DH1' between the -cref and the path. -cref expects only a file, or the path to a file.
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