percentage coverage after alignment

[johnsequence]

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

[imilne]

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).

[drio]

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.

[KevinLam]

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

[imilne]

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.

[bioinfosm]

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!

[imilne]

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

[KevinLam]

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!

[imilne]

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

[bioinfosm]

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..