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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!-
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM -
With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.
Introduction
Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...05-22-2026, 06:42 AM
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