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
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Originally posted by johnsequence View PostHow to calculate the percentage of alignment match after mapping in FASTQ format? Thanks.
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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Originally posted by imilne View PostNot 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).
is BAM - A BAM file is a highly compressed, binary version of SAM. supported by tablet? it doesn't say explicitly
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Originally posted by KevinLam View PostNeat.
is BAM - A BAM file is a highly compressed, binary version of SAM. supported by tablet? it doesn't say explicitlyOur software: Tablet | Flapjack | Strudel | CurlyWhirly | TOPALi
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Originally posted by bioinfosm View PostI am very excited to use tablet, just cautious of its performance of human genome mapped reads!
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 | TOPALi
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Originally posted by imilne View PostHeh, 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
Well we just have to wait for someone to write a 'fam' for indexed reference genomes then!
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Originally posted by KevinLam View PostWow, netbook that's pretty impressive!
Well we just have to wait for someone to write a 'fam' for indexed reference genomes then!
IainOur software: Tablet | Flapjack | Strudel | CurlyWhirly | TOPALi
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Originally posted by imilne View PostHeh, 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
I liked the way tablet worked..--
bioinfosm
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