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  • percentage coverage after alignment

    How to calculate the percentage of alignment match after mapping in FASTQ format? Thanks.

  • #2
    Not quite sure if it's what you're after but Tablet (http://bioinf.scri.ac.uk/tablet) will give you the percentage mismatch for a contig (read bases vs consensus bases, averaged over every read).
    Our software: Tablet | Flapjack | Strudel | CurlyWhirly | TOPALi

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    • #3
      Originally posted by johnsequence View Post
      How to calculate the percentage of alignment match after mapping in FASTQ format? Thanks.
      your mapping out is in fastq format? Define % of alignment match.
      You should dump your alignments in [S|B]AM and then write your own
      tool to report stats. samtools has flagstat (too cryptic for my taste).
      dnaa (dnaa.sourceforge.net -- dnaa/dbamstats).

      Ultimately I suggest you use any of the samtools APis and write your
      own stats tool.
      -drd

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      • #4
        Originally posted by imilne View Post
        Not quite sure if it's what you're after but Tablet (http://bioinf.scri.ac.uk/tablet) will give you the percentage mismatch for a contig (read bases vs consensus bases, averaged over every read).
        Neat.
        is BAM - A BAM file is a highly compressed, binary version of SAM. supported by tablet? it doesn't say explicitly
        http://kevin-gattaca.blogspot.com/

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        • #5
          Originally posted by KevinLam View Post
          Neat.
          is BAM - A BAM file is a highly compressed, binary version of SAM. supported by tablet? it doesn't say explicitly
          Yep, it's supported (since the last version). I'll update that page to say so too.
          Our software: Tablet | Flapjack | Strudel | CurlyWhirly | TOPALi

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          • #6
            Originally posted by imilne View Post
            Yep, it's supported (since the last version). I'll update that page to say so too.
            I am very excited to use tablet, just cautious of its performance of human genome mapped reads!
            --
            bioinfosm

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            • #7
              Originally posted by bioinfosm View Post
              I am very excited to use tablet, just cautious of its performance of human genome mapped reads!
              Heh, cautious in what way?

              We've had 100GB+ bam files loaded into Tablet ok on a 1GB Eee netbook. For now, bam isn't the problem, it's the reference data, which still isn't cached. We do have very efficient in-memory storage (approx 4x compression) but obviously with 100s of megabases of reference sequence that's still a *lot* of data.

              Iain
              Our software: Tablet | Flapjack | Strudel | CurlyWhirly | TOPALi

              Comment


              • #8
                Originally posted by imilne View Post
                Heh, cautious in what way?

                We've had 100GB+ bam files loaded into Tablet ok on a 1GB Eee netbook. For now, bam isn't the problem, it's the reference data, which still isn't cached. We do have very efficient in-memory storage (approx 4x compression) but obviously with 100s of megabases of reference sequence that's still a *lot* of data.

                Iain
                Wow, netbook that's pretty impressive!
                Well we just have to wait for someone to write a 'fam' for indexed reference genomes then!
                http://kevin-gattaca.blogspot.com/

                Comment


                • #9
                  Originally posted by KevinLam View Post
                  Wow, netbook that's pretty impressive!
                  Well we just have to wait for someone to write a 'fam' for indexed reference genomes then!
                  I believe there is .fai for indexed fasta. We just haven't had a chance to look at it, or other options.

                  Iain
                  Our software: Tablet | Flapjack | Strudel | CurlyWhirly | TOPALi

                  Comment


                  • #10
                    Originally posted by imilne View Post
                    Heh, cautious in what way?

                    We've had 100GB+ bam files loaded into Tablet ok on a 1GB Eee netbook. For now, bam isn't the problem, it's the reference data, which still isn't cached. We do have very efficient in-memory storage (approx 4x compression) but obviously with 100s of megabases of reference sequence that's still a *lot* of data.

                    Iain
                    some visualization tools tend to freeze the system!
                    I liked the way tablet worked..
                    --
                    bioinfosm

                    Comment

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