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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!-
Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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