[mira_talk] empty info files with sssip=1
- From: David Lambert <dlamber2@xxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 04 Dec 2009 17:15:41 -0500
Dear Mira users,
I am trying to assemble an EST data set with around 10K sanger reads
and a titanium 454 run. Because unassembled singleton sequences are
likely to be rare but real transcript fragments, I would like to save
them. When I run MIRA with:
miraSearchESTSNPs -project=test2 -fasta
-job=denovo,est,normal,sanger,454 SANGER_SETTINGS -OUT:sssip=1
454_SETTINGS -OUT:sssip=1
the file test2_info_assembly.txt is empty, and so is the file
test2_info_debrislist.txt and I can't find the singletons in the
fasta file or anywhere else. This happens whether I use mira or
miraSearchESTSNPs, and when I run the same assembly without the sssip
parameters, the files are there.
Any suggestions are appreciated, I am stuck.
Thanks,
David Lambert
-------------------------------------------------------------------------
David Lambert
Assistant Professor
Department of Biology
University of Rochester
http://www.rochester.edu/College/BIO/labs/LambertLab/index.html
585 273-2482 (office)
585 275-7521 (lab)
585 275-2070 (fax)
Shipping address:
University of Rochester
Department of Biology
213 Hutchison Hall
River Campus
Rochester, NY 14627-0211
Mailing address:
University of Rochester
Hutchison Hall
RC Box # 270211
Rochester NY 14627-0211
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