Nico,
The main short read aligner in Bioconductor is called matchPDict from
the Biostrings package. It is comparable in speed to MAQ. The
pairwiseAlignment function is intended to provide a flexible alignment
framework for exploration rather than pipeline integration.
Patrick
João Fadista wrote:
Hi,
Dan Koboldt will present a poster at this year's Marco Island sequencing meeting evaluating short read aligners. He has compiled a partial list of aligners at: http://www.massgenomics.org/2009/01/short-read-aligners-update-at-agbt.html
Cheers,
João
-----Original Message-----
From: [email protected]
[mailto:[email protected]] On Behalf Of [email protected]
Sent: Thursday, January 22, 2009 9:51 AM
To: Martin Morgan
Cc: [email protected]
Subject: Re: [Bioc-sig-seq] Filtering Bowtie alignments (has nosubject before)
Hi Martin,
Thanks for that! Sorry that I forgot to put a subject in the original post.
I'm currently looking for some serious benchmarking of the different alignment
software available (maq, bowtie, zoom, pairwiseAlignment in R, etc...) and
although I've been scanning the literature and forums quite a lot, I didn't
find anything done recently. Has anybody heard of something like that?
Cheers,
Nico
Quoting Martin Morgan <[email protected]>:
Hi --
[email protected] writes:
Hi,
I'm currently comparing the alignment generated by bowtie and maq on
the data used in the HilbertVis pdf file of the ShortRead package
(NCBI SRA
accession:
SRA000206). From the original .seq and .prb solexa files, I have
generated the fastq files and aligned them to the ref. genome using
bowtie and maq.
I load both map files in R using readAligned. Then when filtering my
reads, I realized that most of the default filter functions have been
written for maq and are therefore not necessarily available for
bowtie.
Not really for MAQ, but you're right that the filters make assumptions
about data available for filtering.
I'm actually interested in the alignQualityFilter in order to sort
those reads which map several times in the genome (as described in
the page 22 of the "I/0 and Quality Assessment using ShortRead" of
last November bioC tutorial session). But, this method relies on the
quality slot of the object returned by the alignQuality accessor,
which is NA in the case of a bowtie alignment. This is actually
normal, as the final quality mapping value stored in this object is
only available in the maq map file and now in the bowtie one.
So I'd just would like to know if there would be another way to
filter out the reads mapping multiple times in the genome when using
an AlignedRead object obtained from a bowtie map file.
Sorry that this sounds quite confusing... Here is the actual code and
what
happens:
filt <- alignQualityFilter(threshold=1)
# works
aln<-readAligned( "H3K4me1", "run13_lane4.map", type="MAQMap",
filter=filt)
# fails
aln2<-readAligned( "H3K4me1.bowtie", "run13_lane4.map",
type="Bowtie",
filter=filt)
As far as I can tell, Bowtie relies on the read identifier being
unique for each read. So you can
aln2 <- readAligned("H3K4me1.bowtie", "run13_lane4.map",
type="Bowtie")
aln2[!srduplicated(id(aln2))]
Several important caveats. This requires ShortRead >1.1.37 (available
in svn now, with BiocLite Wednesday after about 1 Seattle time, all
being well; the original bowtie parser [intentionally] ignored the
id). Note that the above keeps the _first_ of the duplicated
identifiers; MAQ chooses a random read to report (though the random
number can be set on the MAQ run and hence obtain repeatable results,
or all alignments can be printed out, but the MAQ format when
reporting all reads is, I believe, different from that expected by
ShortRead and readAligned).
You can create your own more elaborate filters, and define them (e.g.,
to be used in readAligned) with the srFilter function, see ?srFilter
for an example.
Hope that helps,
Martin
Error in x...@ranges[i] : subscript contains NAs
Any ideas how to filter a bowtie type alignment for reads mapping
multiple time in the genome?
Cheers,
N.
sessionInfo()
R version 2.9.0 Under development (unstable) (2009-01-04 r47472)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_U
S.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC
_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDE
NTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] HilbertVis_1.1.4 ShortRead_1.1.33 lattice_0.17-20 BSgenome_1.11.8
[5] Biobase_2.3.9 Biostrings_2.11.22 IRanges_1.1.33
loaded via a namespace (and not attached):
[1] grid_2.9.0 Matrix_0.999375-17 tools_2.9.0
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center 1100
Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
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