hiii all, i have a paired end data with each read having 100nt
i am using ./bowtie2 -q -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 -x mygenome -1 a.fastq -2 b.fastq
while using this command do i have to specify the -M 1 option as well since i want only 1 best valid alignment?
wht is the benefit of getting the output in sam format?
A) http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
Presets: setting many settings at once "Bowtie 2 comes with some useful combinations of parameters packaged into shorter "preset" parameters. For example, running Bowtie 2 with the --very-sensitive option is the same as running with options: -D 20 -R 3 -N 0 -L 20 -i S,1,0.50."
Default mode: search for multiple alignments, report the best one By default, Bowtie 2 searches for distinct, valid alignments for each read. When it finds a valid alignment, it generally will continue to look for alignments that are nearly as good or better. It will eventually stop looking, either because it exceeded a limit placed on search effort (see -D and -R) or because it already knows all it needs to know to report an alignment. Information from the best alignments are used to estimate mapping quality (the MAPQ SAM field) and to set SAM optional fields, such as AS:i and XS:i. Bowtie 2 does not gaurantee that the alignment reported is the best possible in terms of alignment score.
The sensitivity does not influence the reporting (directly). By default bowtie2 reports one alignment.
B) SAM is a published specification in which alignments can be reported. The benefit is that more and more downstream tools (e.g. GATK, MACS, genome browsers) directly accept this as input. Actually its most of the time sorted and indexed BAM - which is the binary aequivalent of SAM -, so you might have to put in more effort, but bam conversion and sorting can be done by piping.
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version 2.3.6
hey thank you for the explanation. the problem is when i am using --very-sensitive mode with out -M 1 option included in it, it has just produced a 17gb data as an output but when i included that option it has given me 2.2 gb data so i am wondering. even if i am not mentioned by default bowtie would take -M 3 am i correct?
The -M switch is gone in the latest version, beta7
oh k thank you anyways