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Aligners characterize their degree of confidence in the point oforigin by reporting a mapping quality: a non-negative integer Q = -10log10 p, where p is an estimate of the probability that the alignmentdoes not correspond to the read's true point of origin. Mapping qualityis sometimes abbreviated MAPQ, and is recorded in the SAMMAPQ field.
A "paired-end" or "mate-pair" read consists of pair of mates, calledmate 1 and mate 2. Pairs come with a prior expectation about (a) therelative orientation of the mates, and (b) the distance separating themon the original DNA molecule. Exactly what expectations hold for a givendataset depends on the lab procedures used to generate the data. Forexample, a common lab procedure for producing pairs is Illumina'sPaired-end Sequencing Assay, which yields pairs with a relativeorientation of FR ("forward, reverse") meaning that if mate 1 came fromthe Watson strand, mate 2 very likely came from the Crick strand andvice versa. Also, this protocol yields pairs where the expected genomicdistance from end to end is about 200-500 base pairs.
For simplicity, this manual uses the term "paired-end" to refer toany pair of reads with some expected relative orientation and distance.Depending on the protocol, these might actually be referred to as"paired-end" or "mate-paired." Also, we always refer to the individualsequences making up the pair as "mates."
Pairs are often stored in a pair of files, one file containing themate 1s and the other containing the mates 2s. The first mate in thefile for mate 1 forms a pair with the first mate in the file for mate 2,the second with the second, and so on. When aligning pairs with Bowtie2, specify the file with the mate 1s mates using the -1 argument and the file withthe mate 2s using the -2argument. This causes Bowtie 2 to take the paired nature of the readsinto account when aligning them.
When Bowtie 2 prints a SAM alignment for a pair, it prints tworecords (i.e. two lines of output), one for each mate. The first recorddescribes the alignment for mate 1 and the second record describes thealignment for mate 2. In both records, some of the fields of the SAMrecord describe various properties of the alignment; for instance, the7th and 8th fields (RNEXT and PNEXTrespectively) indicate the reference name and position where the othermate aligned, and the 9th field indicates the inferred length of the DNAfragment from which the two mates were sequenced. See the SAM specificationfor more details regarding these fields.
A pair that aligns with the expected relative mate orientation andwith the expected range of distances between mates is said to align"concordantly". If both mates have unique alignments, but the alignmentsdo not match paired-end expectations (i.e. the mates aren't in theexpected relative orientation, or aren't within the expected distancerange, or both), the pair is said to align "discordantly". Discordantalignments may be of particular interest, for instance, when seeking structuralvariants.
The expected relative orientation of the mates is set using the --ff, --fr, or --rf options. The expectedrange of inter-mates distances (as measured from the furthest extremesof the mates; also called "outer distance") is set with the -I and -X options. Note that setting-I and -X far apart makes Bowtie 2slower. See documentation for -I and -X.
If Bowtie 2 cannot find a paired-end alignment for a pair, by defaultit will go on to look for unpaired alignments for the constituent mates.This is called "mixed mode." To disable mixed mode, set the --no-mixed option.
The SAM FLAGS field, the second field in a SAM record,has multiple bits that describe the paired-end nature of the read andalignment. The first (least significant) bit (1 in decimal, 0x1 inhexadecimal) is set if the read is part of a pair. The second bit (2 indecimal, 0x2 in hexadecimal) is set if the read is part of a pair thataligned in a paired-end fashion. The fourth bit (8 in decimal, 0x8 inhexadecimal) is set if the read is part of a pair and the other mate inthe pair had at least one valid alignment. The sixth bit (32 in decimal,0x20 in hexadecimal) is set if the read is part of a pair and the othermate in the pair aligned to the Crick strand (or, equivalently, if thereverse complement of the other mate aligned to the Watson strand). Theseventh bit (64 in decimal, 0x40 in hexadecimal) is set if the read ismate 1 in a pair. The eighth bit (128 in decimal, 0x80 in hexadecimal)is set if the read is mate 2 in a pair. See the SAM specificationfor a more detailed description of the FLAGS field.
These defaults can be overridden. Setting --no-overlap causesBowtie 2 to consider overlapping mates as non-concordant. Setting --no-contain causesBowtie 2 to consider cases where one mate alignment contains the otheras non-concordant. Setting --dovetail causesBowtie 2 to consider cases where the mate alignments dovetail asconcordant.
By default, Bowtie 2 searches for distinct, valid alignments for eachread. When it finds a valid alignment, it generally will continue tolook for alignments that are nearly as good or better. It willeventually stop looking, either because it exceeded a limit placed onsearch effort (see -D and-R) or because it alreadyknows all it needs to know to report an alignment. Information from thebest alignments are used to estimate mapping quality (theMAPQ SAM field) and toset SAM optional fields, such as AS:i and XS:i. Bowtie 2 doesnot guarantee that the alignment reported is the best possible in termsof alignment score.
In -k mode, Bowtie 2searches for up to N distinct, valid alignments for each read, where Nequals the integer specified with the -k parameter. Thatis, if -k 2 is specified, Bowtie 2 will search for at most2 distinct alignments. It reports all alignments found, in descendingorder by alignment score. The alignment score for a paired-end alignmentequals the sum of the alignment scores of the individual mates. Eachreported read or pair alignment beyond the first has the SAM 'secondary'bit (which equals 256) set in its FLAGS field. Supplementary alignmentswill also be assigned a MAPQ of 255. See the SAM specificationfor details.
-a mode is similar to-k mode except that thereis no upper limit on the number of alignments Bowtie 2 should report.Alignments are reported in descending order by alignment score. Thealignment score for a paired-end alignment equals the sum of thealignment scores of the individual mates. Each reported read or pairalignment beyond the first has the SAM 'secondary' bit (which equals256) set in its FLAGS field. Supplementary alignments will be assigned aMAPQ of 255. See the SAM specificationfor details.
The -p option causesBowtie 2 to launch a specified number of parallel search threads. Eachthread runs on a different processor/core and all threads findalignments in parallel, increasing alignment throughput by approximatelya multiple of the number of threads (though in practice, speedup issomewhat worse than linear).
Comma-separated list of files containing mate 1s (filename usuallyincludes _1), e.g. -1 flyA_1.fq,flyB_1.fq.Sequences specified with this option must correspond file-for-file andread-for-read with those specified in . Reads maybe a mix of different lengths. If - is specified,bowtie2 will read the mate 1s from the "standard in" or"stdin" filehandle.
Comma-separated list of files containing mate 2s (filename usuallyincludes _2), e.g. -2 flyA_2.fq,flyB_2.fq.Sequences specified with this option must correspond file-for-file andread-for-read with those specified in . Reads maybe a mix of different lengths. If - is specified,bowtie2 will read the mate 2s from the "standard in" or"stdin" filehandle.
By default, bowtie2 searches for distinct, validalignments for each read. When it finds a valid alignment, it continueslooking for alignments that are nearly as good or better. The bestalignment found is reported (randomly selected from among best if tied).Information about the best alignments is used to estimate mappingquality and to set SAM optional fields, such as AS:i and XS:i. 2ff7e9595c
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