Difference between revisions of "CH391L/UTpond"
From Marcotte Lab
< CH391L
(→Analysis tool) |
(→Analysis tool) |
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** [http://bioinformatics.oxfordjournals.org/content/25/16/2078.long Paper] | ** [http://bioinformatics.oxfordjournals.org/content/25/16/2078.long Paper] | ||
* SHRiMP: Alignment tool http://compbio.cs.toronto.edu/shrimp/ | * SHRiMP: Alignment tool http://compbio.cs.toronto.edu/shrimp/ | ||
− | ** <b><font color='red'>Never, ever run this program on cygnus. It needs lots of memory, so easily kills the computer.</font></b> | + | ** <b><font color='red'>Never, ever try to run this program on cygnus. It needs lots of memory, so easily kills the computer.</font></b> |
** [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000386 Paper for original version] | ** [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000386 Paper for original version] | ||
** [http://bioinformatics.oxfordjournals.org/content/early/2011/01/28/bioinformatics.btr046 Paper for version 2] | ** [http://bioinformatics.oxfordjournals.org/content/early/2011/01/28/bioinformatics.btr046 Paper for version 2] |
Revision as of 09:41, 25 March 2011
Number of reads
- V3BC21: 213,419 (F3), 199,158 (F5), 223,100 (raw)
- V3BC22: 634,431 (F3), 595,251 (F5), 661,120 (raw)
- V3BC23: 1,015,471 (F3), 951,357 (F5), 1,060,308 (raw)
- V3BC24: 562,803 (F3), 525,892 (F5), 588,304 (raw)
- V3BC25: 569,125 (F3), 531,015 (F5), 595,064 (raw)
Databases
- Prokaryotes:
- Eukaryotes:
- Viruses:
Analysis tool
- SAM : alignment report format
- SHRiMP: Alignment tool http://compbio.cs.toronto.edu/shrimp/
- Never, ever try to run this program on cygnus. It needs lots of memory, so easily kills the computer.
- Paper for original version
- Paper for version 2
$ gsmapper-cs foobar.csfasta db.fasta -E -N 4 -o 1000 -h 80% >foobar.gsmapper_sam 2>foobar.gsmapper_log