| 11 | | {{{ |
| 12 | | bsub "bowtie -k 1 -n 2 -l 70 --best --solexa1.3-quals /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_7.txt ../s7_mouse_mm9.k1.n2.l36.best.map" |
| 13 | | }}} |
| 14 | | |
| 15 | | The parameters used on the sample command are: |
| 16 | | * -l/--seedlen <int> seed length for -n (default: 28) -- Set to longest possible length of high-quality bases. |
| 17 | | * -n/--seedmms <int> max mismatches in seed (can be 0-3, default: -n 2) |
| 18 | | * -k <int> report up to <int> good alignments per read (default: 1) -- If you want only uniquely mapped reads, however, also use '-m 1' to ignore multi-mapped reads |
| 19 | | * --solexa1.3-quals (if input quals are from GA Pipeline ver. >= 1.3)[[br]] |
| 20 | | To find out the solexa version of your reads: [[version_of_solexa_fastq|version_of_solexa_fastq]] |
| 21 | | * --best (in the case of multi-mapped reads, keep only the best hit(s)) |
| 22 | | |
| 23 | | |
| 24 | | Sample command: Output ".sam" file |
| 25 | | {{{ |
| 26 | | bsub "bowtie -k 1 -n 2 -l 70 --best --sam --solexa1.3-quals /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_7.txt ../s7_mouse_mm9.k1.n2.l36.best.sam" |
| 27 | | }}} |
| 28 | | |
| 29 | | Parameters |
| 30 | | * --sam To get SAM output format |
| 31 | | |
| 32 | | To see other parameters log into tak and type '''bowtie''' |
| 33 | | |
| | 10 | * See the [[http://barcwiki.wi.mit.edu/wiki/SOPs/mapping|mapping page]] for more details. |
