[BioC] Amplicon and exon level read counts and GC content

[Martin Morgan]

On 06/07/2012 07:54 AM, Yu Chuan Tai wrote:
> Hi Martin,
>
> Thanks! I will look into the links below. By 'better support for
> paired-end reads in the 'devel' version', which package are you
> referring to?

Mostly GenomicRanges, e.g., readGappedAlignmentPairs, building on 
additional facilities in Rsamtools. Herve is responsible for this.

Martin

>
> Best,
> Yu Chuan
>
> On Thu, 7 Jun 2012, Martin Morgan wrote:
>
>> On 06/06/2012 09:53 PM, Yu Chuan Tai wrote:
>>> Hi Martin,
>>>
>>> More questions on your approaches below. If my BAM files are
>>> generated by Bowtie2 on pair-end fastq files, for scanBamFlag(),
>>> should I set isPaired=TRUE? Do I need to worry about other input
>>> arguments for scanBamFlag() or ScanBamParam(), if I want to
>>> calculate coverage properly?
>>
>> It really depends on what you're interested in doing; see for instance
>> the post by Herve the other day
>>
>> https://stat.ethz.ch/pipermail/bioconductor/2012-June/046052.html
>>
>>>
>>> Also, summarizeOverlaps() doesn't seem to handle paired-end reads.
>>> How to get around this, or it won't affect coverage calculation?
>>
>> There is better support for paired-end reads in the 'devel' version of
>> Biocondcutor; see
>>
>> http://bioconductor.org/developers/useDevel/
>>
>> whether and what aspects of paired-endedness are important depends on
>> how you are using your coverage.
>>
>>>
>>> Finally, is there any way to calculate base-specific coverage at any
>>> genomic locus or interval in Rsamtools? Thanks!
>>
>> I tried to answer this in your other post.
>>
>> Martin
>>
>>>
>>> Best, Yu Chuan
>>>
>>>> More specifically, after
>>>>
>>>> library(Rsamtools) example(scanBam) # defines 'fl', a path to a
>>>> bam file
>>>>
>>>> for a _single_ genomic range
>>>>
>>>> param = ScanBamParam(what="seq", which=GRanges("seq1",
>>>> IRanges(100, 500))) dna = scanBam(fl, param=param)[[1]][["seq"]]
>>>> length(dna) # 365 reads overlap region alphabetFrequency(dna,
>>>> collapse=TRUE, baseOnly=TRUE) # 2838 + 3003 GC
>>>>
>>>> though you'd likely want to specify several regions (vector
>>>> arguments to GRanges) and think about flags (scanBamFlag() and the
>>>> flag argument to ScanBamParam), read mapping quality, reads
>>>> overlapping more than one region, etc. (summarizeOverlaps
>>>> implements several counting strategies, but it is 'easy' to
>>>> implement arbitrary approaches).
>>>>
>>>>>
>>>>> Martin
>>>>>
>>>>>>
>>>>>> Thanks for any input!
>>>>>>
>>>>>> Best, Yu Chuan
>>>>>>
>>>>>> _______________________________________________ Bioconductor
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>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>>>>
>>>>>>
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>>>> Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>>>>
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>>>>
>>
>>
>> --
>> 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
>>


-- 
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