bowtie bowtie_wrapper.py --threads="4" --dataType="solid" --output=$output --suppressHeader=$suppressHeader --genomeSource=$refGenomeSource.genomeSource #if $refGenomeSource.genomeSource == "history": #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ): --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}" --do_not_build_index #else: --ref=$refGenomeSource.ownFile --indexSettings=$refGenomeSource.indexParams.indexSettings #if $refGenomeSource.indexParams.indexSettings == "indexFull": --iautoB=$refGenomeSource.indexParams.autoBehavior.autoB #if $refGenomeSource.indexParams.autoBehavior.autoB == "set": --ipacked=$refGenomeSource.indexParams.autoBehavior.packed --ibmax=$refGenomeSource.indexParams.autoBehavior.bmax --ibmaxdivn=$refGenomeSource.indexParams.autoBehavior.bmaxdivn --idcv=$refGenomeSource.indexParams.autoBehavior.dcv #else: --ipacked="None" --ibmax="None" --ibmaxdivn="None" --idcv="None" #end if --inodc=$refGenomeSource.indexParams.nodc --inoref=$refGenomeSource.indexParams.noref --ioffrate=$refGenomeSource.indexParams.offrate --iftab=$refGenomeSource.indexParams.ftab --intoa=$refGenomeSource.indexParams.ntoa --iendian=$refGenomeSource.indexParams.endian --iseed=$refGenomeSource.indexParams.seed --icutoff=$refGenomeSource.indexParams.cutoff #else: --iautoB="None" --ipacked="None" --ibmax="None" --ibmaxdivn="None" --idcv="None" --inodc="None" --inoref="None" --ioffrate="None" --iftab="None" --intoa="None" --iendian="None" --iseed="None" --icutoff="None" #end if #end if #else: --ref=$refGenomeSource.index --indexSettings="None" --iautoB="None" --ipacked="None" --ibmax="None" --ibmaxdivn="None" --idcv="None" --inodc="None" --inoref="None" --ioffrate="None" --iftab="None" --intoa="None" --iendian="None" --iseed="None" --icutoff="None" #end if --paired=$singlePaired.sPaired #if $singlePaired.sPaired == "single": --input1=$singlePaired.sInput1 --input2="None" --params=$singlePaired.sParams.sSettingsType #if $singlePaired.sParams.sSettingsType == "full": --skip=$singlePaired.sParams.sSkip --alignLimit=$singlePaired.sParams.sAlignLimit --trimH=$singlePaired.sParams.sTrimH --trimL=$singlePaired.sParams.sTrimL --mismatchSeed=$singlePaired.sParams.sMismatchSeed --mismatchQual=$singlePaired.sParams.sMismatchQual --seedLen=$singlePaired.sParams.sSeedLen --rounding=$singlePaired.sParams.sRounding --maqSoapAlign=$singlePaired.sParams.sMaqSoapAlign --tryHard=$singlePaired.sParams.sTryHard --valAlign=$singlePaired.sParams.sValAlign --allValAligns=$singlePaired.sParams.sAllValAligns --suppressAlign=$singlePaired.sParams.sSuppressAlign --best=$singlePaired.sParams.sBestOption.sBest #if $singlePaired.sParams.sBestOption.sBest == "doBest": --maxBacktracks=$singlePaired.sParams.sBestOption.sdMaxBacktracks --strata=$singlePaired.sParams.sBestOption.sdStrata #else: --maxBacktracks=$singlePaired.sParams.sBestOption.snMaxBacktracks --strata="None" #end if --offrate=$singlePaired.sParams.sOffrate --seed=$singlePaired.sParams.sSeed --snpphred=$singlePaired.sParams.sSnpphred --snpfrac=$singlePaired.sParams.sSnpfrac --keepends=$singlePaired.sParams.sKeepends #else: --skip="None" --alignLimit="None" --trimH="None" --trimL="None" --mismatchSeed="None" --mismatchQual="None" --seedLen="None" --rounding="None" --maqSoapAlign="None" --tryHard="None" --valAlign="None" --allValAligns="None" --suppressAlign="None" --best="None" --maxBacktracks="None" --strata="None" --offrate="None" --seed="None" --snpphred="None" --snpfrac="None" --keepends="None" #end if --minInsert="None" --maxInsert="None" --mateOrient="None" --maxAlignAttempt="None" --forwardAlign="None" --reverseAlign="None" #else: --input1=$singlePaired.pInput1 --input2=$singlePaired.pInput2 --maxInsert=$singlePaired.pMaxInsert --mateOrient=$singlePaired.pMateOrient --params=$singlePaired.pParams.pSettingsType #if $singlePaired.pParams.pSettingsType == "full": --skip=$singlePaired.pParams.pSkip --alignLimit=$singlePaired.pParams.pAlignLimit --trimH=$singlePaired.pParams.pTrimH --trimL=$singlePaired.pParams.pTrimL --mismatchSeed=$singlePaired.pParams.pMismatchSeed --mismatchQual=$singlePaired.pParams.pMismatchQual --seedLen=$singlePaired.pParams.pSeedLen --rounding=$singlePaired.pParams.pRounding --maqSoapAlign=$singlePaired.pParams.pMaqSoapAlign --minInsert=$singlePaired.pParams.pMinInsert --maxAlignAttempt=$singlePaired.pParams.pMaxAlignAttempt --forwardAlign=$singlePaired.pParams.pForwardAlign --reverseAlign=$singlePaired.pParams.pReverseAlign --tryHard=$singlePaired.pParams.pTryHard --valAlign=$singlePaired.pParams.pValAlign --allValAligns=$singlePaired.pParams.pAllValAligns --suppressAlign=$singlePaired.pParams.pSuppressAlign --best=$singlePaired.pParams.pBestOption.pBest #if $singlePaired.pParams.pBestOption.pBest == "doBest": --maxBacktracks=$singlePaired.pParams.pBestOption.pdMaxBacktracks --strata=$singlePaired.pParams.pBestOption.pdStrata #else: --maxBacktracks=$singlePaired.pParams.pBestOption.pnMaxBacktracks --strata="None" #end if --offrate=$singlePaired.pParams.pOffrate --seed=$singlePaired.pParams.pSeed --snpphred=$singlePaired.pParams.pSnpphred --snpfrac=$singlePaired.pParams.pSnpfrac --keepends=$singlePaired.pParams.pKeepends #else: --skip="None" --alignLimit="None" --trimH="None" --trimL="None" --mismatchSeed="None" --mismatchQual="None" --seedLen="None" --rounding="None" --maqSoapAlign="None" --minInsert="None" --maxAlignAttempt="None" --forwardAlign="None" --reverseAlign="None" --tryHard="None" --valAlign="None" --allValAligns="None" --suppressAlign="None" --best="None" --maxBacktracks="None" --strata="None" --offrate="None" --seed="None" --snpphred="None" --snpfrac="None" --keepends="None" #end if #end if Use a built-in index Use one from the history Default Set your own Automatic behavior Set values (sets --noauto and allows others to be set) Use regular representation Use packed representation Use difference-cover sample Disable difference-cover sample Build all index files Do not build paired-end alignment index files Do not convert Ns Convert Ns to As Little Big Single-end Paired-end Commonly used Full parameter list Round to nearest 10 Do not round to nearest 10 Do not try hard Try hard Do not report all valid alignments Report all valid alignments Do not use best Use best Do not use strata option Use strata option Keep ends Trim ends FF (for SOLiD) FR (for Illumina) RF Commonly used Full parameter list Round to nearest 10 Do not round to nearest 10 Align against the forward reference strand Do not align against the forward reference strand Align against the reverse-complement reference strand Do not align against the reverse-complement reference strand Do not try hard Try hard Do not report all valid alignments Report all valid alignments Do not use best Use best Do not use strata option Use strata option Keep ends Trim ends

**What it does** Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25. .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml ------ **Know what you are doing** .. class:: warningmark There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy. .. __: http://bowtie-bio.sourceforge.net/index.shtml ------ **Input formats** Bowtie accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files. ------ **Outputs** The output is in SAM format, and has the following columns:: Column Description -------- -------------------------------------------------------- 1 QNAME Query (pair) NAME 2 FLAG bitwise FLAG 3 RNAME Reference sequence NAME 4 POS 1-based leftmost POSition/coordinate of clipped sequence 5 MAPQ MAPping Quality (Phred-scaled) 6 CIGAR extended CIGAR string 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME) 8 MPOS 1-based Mate POSition 9 ISIZE Inferred insert SIZE 10 SEQ query SEQuence on the same strand as the reference 11 QUAL query QUALity (ASCII-33 gives the Phred base quality) 12 OPT variable OPTional fields in the format TAG:VTYPE:VALUE The flags are as follows:: Flag Description ------ ------------------------------------- 0x0001 the read is paired in sequencing 0x0002 the read is mapped in a proper pair 0x0004 the query sequence itself is unmapped 0x0008 the mate is unmapped 0x0010 strand of the query (1 for reverse) 0x0020 strand of the mate 0x0040 the read is the first read in a pair 0x0080 the read is the second read in a pair 0x0100 the alignment is not primary It looks like this (scroll sideways to see the entire example):: QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh ------- **Bowtie settings** All of the options have a default value. You can change any of them. Most of the options in Bowtie have been implemented here. ------ **Bowtie parameter list** This is an exhaustive list of Bowtie options: For indexing (bowtie-build):: -a No auto behavior. Disable the default behavior where bowtie automatically selects values for --bmax/--bmaxdivn/--dcv/--packed parameters according to the memory available. [off] --packed Packing. Use a packed representation for DNA strings. [auto] --bmax INT Suffix maximum. The maximum number of suffixes allowed in a block. [auto] --bmaxdivn INT Suffix maximum fraction. The maximum number of suffixes allowed in a block expressed as a fraction of the length of the reference. [4] --dcv INT Difference-cover sample. Use INT as the period for the difference-cover sample. [1024] --nodc INT No difference-cover sample. Disable the difference-cover sample. [off] -r No reference indexes. Do not build the NAME.3.ebwt and NAME.4.ebwt portions of the index. Used only for paired-end alignment. [off] -o Offrate. How many Burrows-Wheeler rows get marked by the indexer. The indexer will mark every 2^INT rows. The marked rows correspond to rows on the genome. [5] -t INT Ftab. The lookup table used to calculate an initial Burrows-Wheeler range with respect to the first INT characters of the query. Ftab is 4^INT+1 bytes. [10] --ntoa N conversion. Convert Ns to As before building the index. Otherwise, Ns are simply excluded from the index and Bowtie will not find alignments that overlap them. [off] --big Endianness. Endianness to use when serializing integers to the index file. [off] --little Endianness. [--little] --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off] --cutoff INT Cutoff. Index only the first INT bases of the reference sequences (cumulative across sequences) and ignore the rest. [off] For aligning (bowtie):: -s INT Skip. Do not align the first INT reads or pairs in the input. [off] -u INT Align limit. Only align the first INT reads/pairs from the input. [no limit] -5 INT High-quality trim. Trim INT bases from the high-quality (left) end of each read before alignment. [0] -3 INT Low-quality trim. Trim INT bases from the low-quality (right) end of each read before alignment. [0] -n INT Mismatch seed. Maximum number of mismatches permitted in the seed (defined with seed length option). Can be 0, 1, 2, or 3. [2] -e INT Mismatch quality. Maximum permitted total of quality values at mismatched read positions. Bowtie rounds quality values to the nearest 10 and saturates at 30. [70] -l INT Seed length. The number of bases on the high-quality end of the read to which the -n ceiling applies. Must be at least 5. [28] --nomaqround Suppress MAQ rounding. Values are internally rounded to the nearest 10 and saturate at 30. This options turns off that rounding. [off] -v INT MAQ- or SOAP-like alignment policy. This option turns off the default MAQ-like alignment policy in favor of a SOAP-like one. End-to-end alignments with at most INT mismatches. [off] -I INT Minimum insert. The minimum insert size for valid paired-end alignments. Does checking on untrimmed reads if -5 or -3 is used. [0] -X INT Maximum insert. The maximum insert size for valid paired-end alignments. Does checking on untrimmed reads if -5 or -3 is used. [250] --fr Mate orientation. The upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand. [--fr] --rf Mate orientation. [off] --ff Mate orientation. [off] --pairtries INT Maximum alignment attempts for paired-end data. [100] --nofw No forward aligning. Choosing this option means that Bowtie will not attempt to align against the forward reference strand. [off] --norc No reverse-complement aligning. Setting this will mean that Bowtie will not attempt to align against the reverse-complement reference strand. [off] --maxbts INT Maximum backtracks. The maximum number of backtracks permitted when aligning a read in -n 2 or -n 3 mode. [125 without --best] [800 with --best] -y Try hard. Try as hard as possible to find valid alignments when they exist, including paired-end alignments. [off] --chunkmbs INT Thread memory. The number of megabytes of memory a given thread is given to store path descriptors in --best mode. [32] -k INT Valid alignments. The number of valid alignments per read or pair. [off] -a All valid alignments. Choosing this means that all valid alignments per read or pair will be reported. [off] -m INT Suppress alignments. Suppress all alignments for a particular read or pair if more than INT reportable alignments exist for it. [no limit] --best Best mode. Make Bowtie guarantee that reported singleton alignments are "best" in terms of stratum (the number of mismatches) and quality values at mismatched position. [off] --strata Best strata. When running in best mode, report alignments that fall into the best stratum if there are ones falling into more than one. [off] -o INT Offrate override. Override the offrate of the index with INT. Some row markings are discarded when index read into memory. INT must be greater than the value used to build the index (default: 5). [off] --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off] --snpphred INT Use INT as the SNP penalty for decoding colorspace alignments. True ratio of SNPs per base in the subject genome. [see --snpfrac] --snpfrac DEC Use DEC as the estimated ratio of SNPs per base when decoding colorspace alignments. [0.001] --col-keepends Keep the extreme-end nucleotides and qualities when decoding colorspace alignments. [off]