Difference between revisions of "CH391L/UTpond"
From Marcotte Lab
< CH391L
(→Analysis tool) |
(→Number of reads) |
||
Line 5: | Line 5: | ||
* V3BC24: 562,803 (F3), 525,892 (F5), 588,304 (raw) | * V3BC24: 562,803 (F3), 525,892 (F5), 588,304 (raw) | ||
* V3BC25: 569,125 (F3), 531,015 (F5), 595,064 (raw) | * V3BC25: 569,125 (F3), 531,015 (F5), 595,064 (raw) | ||
+ | You can download CSFASTA files from [http://www.marcottelab.org/users/CH391L/UTpond/raw/ here]. | ||
== Databases == | == Databases == |
Revision as of 16:32, 28 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)
You can download CSFASTA files from here.
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