Comments for MassGenomics

Comment on Short Read Aligners: Maq, Eland, and Others by jhui

jhui — Thu, 19 Jun 2008 20:19:50 +0000

SeqMap (http://biogibbs.stanford.edu/~jiangh/SeqMap/) - work like ELand, can do 3 or more bp mismatches and also insdel

Comment on Short Read Aligners: Maq, Eland, and Others by Subcutaneous

Subcutaneous — Thu, 19 Jun 2008 04:07:29 +0000

Somehow i missed the point. Probably lost in translation Anyway … nice blog to visit.

cheers, Subcutaneous.

Comment on Short Read Aligners: Maq, Eland, and Others by zayedi

zayedi — Tue, 17 Jun 2008 09:29:41 +0000

I’m still not so keen on using eland in situations when my reads are less than 25bp but greater than 20bp e.g with microRNAs sequenced from Solexa. The FP question can only reliably answered on testing various scenarios where we actually know where our reads will map.
Something I’ve also seen is that you may not align a read where there are ambiguous characters around the mid-section of the short sequence read.
Using paired-end will definitely push up FP but with higher read errors, indels, etc, the curve for PE alignment may look better.

Comment on Short Read Aligners: Maq, Eland, and Others by John Castle

John Castle — Thu, 12 Jun 2008 00:07:10 +0000

Has anyone tested Biostrings (in Bioconductor) or qpalma(http://www.fml.tuebingen.mpg.de/raetsch/projects/qpalma/qpalma-final.pdf) [uses Vmatch]?

Comment on About by Deanne Taylor

Deanne Taylor — Fri, 23 May 2008 17:44:09 +0000

Thanks for all the great posts! I think our interests overlap.

Comment on Short Read Aligners: Maq, Eland, and Others by Sparks

Sparks — Thu, 22 May 2008 07:05:59 +0000

To:ac
I can think of two drawbacks on using Eland as a preprocess to maq.
First is that you won’t pick up any short indels with Eland, only SNPs so if you remove NM reads you might miss any short indel polymorphisms.
Second is that Eland can align with max of 2 mismatches where maq can handle more. Again only problem if you remove NM reads.
You could consider retaining NM reads for input to maq.

Comment on Short Read Aligners: Maq, Eland, and Others by ac

ac — Mon, 19 May 2008 15:36:09 +0000

“The main contributor (other is read quality) to FPs is repeats or near repeats so a read has alternative alignment locations. Sometimes this will result in one alignment which may turn out to be a FP. Sometimes we’ll get multiple alignments with the same score. With MAQ, its habit of randomly choosing one alignment from a set of equal scoring alignments introduces some FP and some extra (random) TP. Other tools just report the read as having multiple alignments which some evaluations report as a FN.”

We generally get around this by providing only uniquely aligned reads from Eland as input to MAQ. The obvious drawback to this is that you may be losing some reads. However, I haven’t seen any drop in depth beyond 1X unless it is a highly repetitive region. Fortunately we did see some FPs go away with this approach but does anyone see any drawbacks?

Comment on Short Read Aligners: Maq, Eland, and Others by Justin

Justin — Mon, 19 May 2008 03:26:29 +0000

I am under the impression that the random assignment protocol in MAQ for repeats results in a lower mapping quality score for such assigned reads.

Can anyone here point me in a direction to understand how SNP calling is conditioned on mapping quality score for MAQ?

I couldn’t find it on the MAQ page.

Comment on Short Read Aligners: Maq, Eland, and Others by MB

MB — Fri, 16 May 2008 20:47:37 +0000

At the current version, eland itself does not do paired end alignment, but there is other scripts in the GAPipeline which can achieve this by post-processing eland output. Another script calculate mapping qualities. Unfortunately, not many people know how to use them as they have not been well documented, so far as I know.

In addition, it is easy to benchmark alignment, but it is quite hard to bechmark SNP calling with simulation. A lot of troubles that cause wrong SNPs can hardly be simulated accurately as people are simply not aware of them.

Comment on Short Read Aligners: Maq, Eland, and Others by Sparks

Sparks — Fri, 16 May 2008 00:58:33 +0000

The main contributor (other is read quality) to FPs is repeats or near repeats so a read has alternative alignment locations. Sometimes this will result in one alignment which may turn out to be a FP. Sometimes we’ll get multiple alignments with the same score. With MAQ, its habit of randomly choosing one alignment from a set of equal scoring alignments introduces some FP and some extra (random) TP. Other tools just report the read as having multiple alignments which some evaluations report as a FN.