Difference between revisions of "Bowtie (analysis)"

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:[[Biouml.plugins.bowtie (plugin)|biouml.plugins.bowtie (Bowtie plugin)]]

Revision as of 11:13, 31 May 2013

Analysis title
BSA-Bowtie-icon.png Bowtie
Provider
Institute of Systems Biology
Class
BowtieAnalysis
Plugin
biouml.plugins.bowtie (Bowtie plugin)

Description

This analysis allows you to align large sets of short DNA sequences (reads) to large genomes.

Parameters:

  • Input sequences – Collection containing input reads
  • Input sequences (fastq files) – Input sequences in fastq files
  • Species – Species
  • Default alignment parameters – Default alignment parameters
  • Alignment parameters – Alignment parameters
    • Number of mismatches – Number of mismatches (0, 1, 2 or 3)
    • Seed length – Seed length (at least 5)
    • Total error – Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment
    • No MAQ round – Prevent MAQ rounding of base qualities
    • Max backtracks – The maximum number of backtracks permitted when aligning a read
    • All alignments – Report all valid alignments per read
    • Max alignments per read – Report up to N valid alignments per read
    • Remove redundant alignments – Suppress all alignments for a particular read if more than 'redundantAlignment' reportable alignments exist for it
    • Number of alignemnts for read to be considered redundant – Number of alignemnts for read to be considered redundant
    • Best – Best
    • Stratum – Stratum
  • Thread count (expert) – Thread count
  • Minimal output (expert) – Output just genomic coordinates(no read sequence, alignment quality and so on)
  • Use shared memory (expert) – Permanently place genome index into shared memory
  • Output track – Specify where to store an output

More about Bowtie at: http://bowtie-bio.sourceforge.net/index.shtml.

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