Salmonella: Difference between revisions
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(→SPA) |
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== SPA == | == SPA == | ||
# Traces: | |||
All directories: 103971 (unique) | |||
B_SPA : 102405 (unique) => 1566 missing | |||
Best assembly: | Best assembly: | ||
| Line 18: | Line 22: | ||
CO Contig1368 4813926 88824 1869182 C | CO Contig1368 4813926 88824 1869182 C | ||
!!! Other Salmonella's are also 4.8M | !!! Other Salmonella's are also 4.8M | ||
Conversion: | |||
$ cat B_SPA.mates | |||
library small 2000 4000 .* | |||
pair p(.*).b1$ p(.*).g1$ | |||
library medium 4500 5500 .* | |||
pair oyg(.*).b1$ oyg(.*).g1$ | |||
library large 35000 45000 .* | |||
pair P_AA(.*).b1$ P_AA(.*).g1$ | |||
$ toAmos -m B_SPA.mates -ace B_SPA.fasta.screen.ace.83 -o B_SPA.afg | |||
$ bank-transact -b B_SPA.bnk -m B_SPA.afg -c | |||
Revision as of 00:22, 22 October 2007
Data
Strain:
Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150: B_SPA Salmonella typhimurium LT2 : B_STM
File locations:
/fs/ftp-cbcb/pub/data/dsommer/ /fs/szasmg/Bacteria/Salmonella/ /tmp/B_SPA (host: sycamore)
SPA
- Traces:
All directories: 103971 (unique) B_SPA : 102405 (unique) => 1566 missing
Best assembly:
B_SPA/edit_dir/B_SPA.fasta.screen.ace.83
File location:
/tmp/B_SPA/edit_dir/B_SPA.fasta.screen.ace.83
Longest contig:
CO Contig1368 4813926 88824 1869182 C !!! Other Salmonella's are also 4.8M
Conversion:
$ cat B_SPA.mates
library small 2000 4000 .* pair p(.*).b1$ p(.*).g1$ library medium 4500 5500 .* pair oyg(.*).b1$ oyg(.*).g1$ library large 35000 45000 .* pair P_AA(.*).b1$ P_AA(.*).g1$
$ toAmos -m B_SPA.mates -ace B_SPA.fasta.screen.ace.83 -o B_SPA.afg $ bank-transact -b B_SPA.bnk -m B_SPA.afg -c