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howto:bioinformatics:bowtie [2013/11/22 13:41]
dane [Job script] |
— (current) |
| ====== Running Bowtie ====== | |
| |
| ===== Before you start ===== | |
| Before running your scripts remember to run((Note: Make sure the line:<code bash>export MODULEPATH=/opt/gridware/bioinformatics/modules:$MODULEPATH</code>exists in your //~/.profile// file)):<code bash>user@login01:~ $ module add bowtie/1.0.0</code> | |
| |
| ===== Job script ===== | |
| Then your job script called //my_job.msub// will look something like this: | |
| <file bash my_job.msub> | |
| #/bin/sh | |
| #MSUB -l nodes=1:ppn=12 | |
| #MSUB -l feature=dell | |
| #MSUB -l walltime=10:00:00 | |
| #MSUB -m be | |
| #MSUB -V | |
| #MSUB -o ${HOME}/scratch5/BOWTIE/stdout.txt | |
| #MSUB -e ${HOME}/scratch5/BOWTIE/stderr.txt | |
| #MSUB -d ${HOME}/scratch5/BOWTIE/ | |
| #MSUB -N MyBowtieJob | |
| #MSUB -mb | |
| |
| NP=`cat ${PBS_NODEFILE} | wc -l` | |
| |
| EXE="bowtie" | |
| forward_reads="A_reads1.fq,B_reads_1.fq" | |
| reverse_reads="A_reads1.fq,B_reads_1.fq" | |
| output_file="piggy_hits.sam" | |
| ARGS="sscrofa --shmem --threads ${NP} --sam -q -1 ${forward_reads} -2 ${reverse_reads} ${output_file}" | |
| |
| ${EXE} ${ARGS} | |
| </file> | |
| |
| ===== Submit your job ===== | |
| Finally submit your job using:<code bash>user@login01:~ $ msub my_job.msub</code> | |
| |
| ===== Bowtie help ===== | |
| obtained by running:<code bash>user@login01:~ $ bowtie -h</code> | |
| |
| ==== Usage ==== | |
| <code> | |
| bowtie [options]* <ebwt> {-1 <m1> -2 <m2> | --12 <r> | <s>} [<hit>] | |
| |
| <m1> Comma-separated list of files containing upstream mates (or the | |
| sequences themselves, if -c is set) paired with mates in <m2> | |
| <m2> Comma-separated list of files containing downstream mates (or the | |
| sequences themselves if -c is set) paired with mates in <m1> | |
| <r> Comma-separated list of files containing Crossbow-style reads. Can be | |
| a mixture of paired and unpaired. Specify "-" for stdin. | |
| <s> Comma-separated list of files containing unpaired reads, or the | |
| sequences themselves, if -c is set. Specify "-" for stdin. | |
| <hit> File to write hits to (default: stdout) | |
| </code> | |
| ==== Options ==== | |
| === Input === | |
| <code> | |
| -q query input files are FASTQ .fq/.fastq (default) | |
| -f query input files are (multi-)FASTA .fa/.mfa | |
| -r query input files are raw one-sequence-per-line | |
| -c query sequences given on cmd line (as <mates>, <singles>) | |
| -C reads and index are in colorspace | |
| -Q/--quals <file> QV file(s) corresponding to CSFASTA inputs; use with -f -C | |
| --Q1/--Q2 <file> same as -Q, but for mate files 1 and 2 respectively | |
| -s/--skip <int> skip the first <int> reads/pairs in the input | |
| -u/--qupto <int> stop after first <int> reads/pairs (excl. skipped reads) | |
| -5/--trim5 <int> trim <int> bases from 5' (left) end of reads | |
| -3/--trim3 <int> trim <int> bases from 3' (right) end of reads | |
| --phred33-quals input quals are Phred+33 (default) | |
| --phred64-quals input quals are Phred+64 (same as --solexa1.3-quals) | |
| --solexa-quals input quals are from GA Pipeline ver. < 1.3 | |
| --solexa1.3-quals input quals are from GA Pipeline ver. >= 1.3 | |
| --integer-quals qualities are given as space-separated integers (not ASCII) | |
| </code> | |
| === Alignment === | |
| <code> | |
| -v <int> report end-to-end hits w/ <=v mismatches; ignore qualities | |
| or | |
| -n/--seedmms <int> max mismatches in seed (can be 0-3, default: -n 2) | |
| -e/--maqerr <int> max sum of mismatch quals across alignment for -n (def: 70) | |
| -l/--seedlen <int> seed length for -n (default: 28) | |
| --nomaqround disable Maq-like quality rounding for -n (nearest 10 <= 30) | |
| -I/--minins <int> minimum insert size for paired-end alignment (default: 0) | |
| -X/--maxins <int> maximum insert size for paired-end alignment (default: 250) | |
| --fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (default: --fr) | |
| --nofw/--norc do not align to forward/reverse-complement reference strand | |
| --maxbts <int> max # backtracks for -n 2/3 (default: 125, 800 for --best) | |
| --pairtries <int> max # attempts to find mate for anchor hit (default: 100) | |
| -y/--tryhard try hard to find valid alignments, at the expense of speed | |
| --chunkmbs <int> max megabytes of RAM for best-first search frames (def: 64) | |
| </code> | |
| === Reporting === | |
| <code> | |
| -k <int> report up to <int> good alignments per read (default: 1) | |
| -a/--all report all alignments per read (much slower than low -k) | |
| -m <int> suppress all alignments if > <int> exist (def: no limit) | |
| -M <int> like -m, but reports 1 random hit (MAPQ=0); requires --best | |
| --best hits guaranteed best stratum; ties broken by quality | |
| --strata hits in sub-optimal strata aren't reported (requires --best) | |
| </code> | |
| === Output === | |
| <code> | |
| -t/--time print wall-clock time taken by search phases | |
| -B/--offbase <int> leftmost ref offset = <int> in bowtie output (default: 0) | |
| --quiet print nothing but the alignments | |
| --refout write alignments to files refXXXXX.map, 1 map per reference | |
| --refidx refer to ref. seqs by 0-based index rather than name | |
| --al <fname> write aligned reads/pairs to file(s) <fname> | |
| --un <fname> write unaligned reads/pairs to file(s) <fname> | |
| --max <fname> write reads/pairs over -m limit to file(s) <fname> | |
| --suppress <cols> suppresses given columns (comma-delim'ed) in default output | |
| --fullref write entire ref name (default: only up to 1st space) | |
| </code> | |
| === Colorspace === | |
| <code> | |
| --snpphred <int> Phred penalty for SNP when decoding colorspace (def: 30) | |
| or | |
| --snpfrac <dec> approx. fraction of SNP bases (e.g. 0.001); sets --snpphred | |
| --col-cseq print aligned colorspace seqs as colors, not decoded bases | |
| --col-cqual print original colorspace quals, not decoded quals | |
| --col-keepends keep nucleotides at extreme ends of decoded alignment | |
| </code> | |
| === SAM === | |
| <code> | |
| -S/--sam write hits in SAM format | |
| --mapq <int> default mapping quality (MAPQ) to print for SAM alignments | |
| --sam-nohead supppress header lines (starting with @) for SAM output | |
| --sam-nosq supppress @SQ header lines for SAM output | |
| --sam-RG <text> add <text> (usually "lab=value") to @RG line of SAM header | |
| </code> | |
| === Performance === | |
| <code> | |
| -o/--offrate <int> override offrate of index; must be >= index's offrate | |
| -p/--threads <int> number of alignment threads to launch (default: 1) | |
| --mm use memory-mapped I/O for index; many 'bowtie's can share | |
| --shmem use shared mem for index; many 'bowtie's can share | |
| </code> | |
| === Other === | |
| <code> | |
| --seed <int> seed for random number generator | |
| --verbose verbose output (for debugging) | |
| --version print version information and quit | |
| -h/--help print this usage message | |
| </code> | |
