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Old 09-28-2011, 09:25 AM   #3
Location: St. Louis, MO

Join Date: May 2011
Posts: 14

thanks very much for all that great advice! The read length is 90 bp. I made your modifications and shortened the read file names (and unzipped them) and now get this error, which I am sure is progress:

pgx:bowtie-0.12.7 rworthi$ ./bowtie -n 2 -S -t -p 2 -X 100 --solexa1.3-quals indexes/hg19 -1 ~/oto-L3_1.fq -2 ~/oto-L3_2.fq bowtie.exome.sam
Time loading reference: 00:00:09
Time loading forward index: 00:00:14
Time loading mirror index: 00:00:14
Warning: Exhausted best-first chunk memory for read FCB0AMFABXX:3:1101:16474:2240#GGCTACAT/1 (patid 400); skipping read
... continuing indefinitely for each line

Do I need a memory switch in the line?
Professor of Pharmaceutical Sciences at Southern Illinois University. Subject of the Personal Genomes Project with CGI genome sequencing, funded by a university seed grant. Annotated human and mouse genomes at the Washington University (St. Louis) GSC during Bob Waterston's tenure. Worked in nematode gene discovery at Divergence, Inc. Recent NSF grant in yeast recombinant genetics. Teach pharmacogenomics, human genomics and pharmaceutical biotechnology.
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