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Old 03-09-2010, 08:08 AM   #1
johnsequence
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Default percentage coverage after alignment

How to calculate the percentage of alignment match after mapping in FASTQ format? Thanks.
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Old 03-09-2010, 09:33 AM   #2
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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).
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Old 03-09-2010, 02:21 PM   #3
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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.
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Old 03-10-2010, 12:51 AM   #4
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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
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Old 03-10-2010, 05:45 AM   #5
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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.
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Old 03-10-2010, 10:50 AM   #6
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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!
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Old 03-11-2010, 02:06 AM   #7
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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
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Old 03-11-2010, 02:16 AM   #8
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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!
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Old 03-11-2010, 02:17 AM   #9
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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.

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Old 03-15-2010, 02:36 PM   #10
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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..
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