[Bioc-sig-seq] readAligned and BAM format

[Martin Morgan]

Hi Wave --

svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsamtools

R CMD INSTALL --clean Rsamtools

see the script in Rsamtools/inst/script/readAligned_prototype.R

e.g.,

  source(system.file("script", "readAligned_prototype.R",
                     package="Rsamtools"))
  .readAligned_bam(<...>) # args like the other readAligned

see ?scanBam for additional ideas.

Martin

Wu Wei wrote:
> Hi Martin,
> 
> I am also looking for that. Would you please also forward that
> additional info to me.
> 
> Thanks,
> Wave
> 
> On 2 Nov 2009, at 14:34, Martin Morgan wrote:
> 
>> Joern Toedling wrote:
>>> Hi everyone,
>>>
>>> has anybody by chance already written a parser for importing
>>> alignments in
>>> BAM/SAM format into objects of class AlignedRead? This format seems
>>> to be
>>> gaining more and more support, yet it is still absent from the
>>> options in
>>> function readAligned. If one of you already has written such a parsing
>>> function and would not mind sharing it, please let me know.
>>
>> Hi Joern -- there is a package in the Bioc svn repository that does
>> this; it is not yet in the devel branch, there are some limitations in
>> terms of AlignedRead (e.g., AlignedRead currently supports only ungapped
>> alignments, whereas BAM allows gapped). I'll forward additional info
>> off-list.
>>
>> Martin
>>>
>>> Best regards,
>>> Joern
>>>
>>> ---
>>> Joern Toedling
>>> Institut Curie -- U900
>>> 26 rue d'Ulm, 75005 Paris, FRANCE
>>> Tel. +33 (0)156246926
>>>
>>> _______________________________________________
>>> Bioc-sig-sequencing mailing list
>>> Bioc-sig-sequencing at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>
>>
>> -- 
>> Martin Morgan
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M1 B861
>> Phone: (206) 667-2793
>>
>> _______________________________________________
>> Bioc-sig-sequencing mailing list
>> Bioc-sig-sequencing at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
> 
> 
> 
> Wu Wei
> Postdoctoral Fellow
> Steinmetz Group, EMBL Heidelberg
> Tex: +49 6221 387-8310 (8114)
> Fax: +49 6221 387-8518
> Email: wuwei at embl.de
> 
> 
> 
> 


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793