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How to calculate the percentage of alignment match after mapping in FASTQ format? Thanks.
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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 -
your mapping out is in fastq format? Define % of alignment match.Originally posted by johnsequence View Post
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.-drdComment
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Neat.Originally posted by imilne View Post
is BAM - A BAM file is a highly compressed, binary version of SAM. supported by tablet? it doesn't say explicitlyComment
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Heh, cautious in what way?Originally posted by bioinfosm View Post
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.
IainOur software: Tablet | Flapjack | Strudel | CurlyWhirly | TOPALiComment
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Wow, netbook that's pretty impressive!Originally posted by imilne View Post
Well we just have to wait for someone to write a 'fam' for indexed reference genomes then!Comment
some visualization tools tend to freeze the system!-
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