 [ This is a repeat email for archive completeness ]

Valerie, thank you for the pointers, I've enjoyed going through the pasilla
workflow.  Martin, thanks for the Rsubread reference, it appears to give a
solid basis for understanding the similarities and differences between
Rsubread, summarizeOverlaps / countOverlaps, htseq-count, and coverageBed.
 This has been very informative, thank you very much for sharing.

_Taku



On Thu, Dec 5, 2013 at 9:03 AM, Valerie Obenchain <vobencha@fhcrc.org>wrote:

> In addition to the resources Martin mentions,
>
>     library(GenomicAlignments)
>     browseVignettes("GenomicAlignments")
>
> gets the 'Counting reads with summarizeOverlaps' vignette. (In the release
> branch this vignette lives in GenomicRanges.) The vignette covers the
> counting modes in detail and includes a workflow with the pasilla data.
>
> Valerie
>
>
>
> On 12/05/2013 08:19 AM, Martin Morgan wrote:
>
>> On 12/05/2013 06:37 AM, Taku Tokuyasu wrote:
>>
>>> Martin, Michael:
>>>
>>> Thank you for the prompt replies!  Glad to know the functionality is
>>> available.
>>>   The suggestions on alternatives are also quite helpful.  Amongst other
>>> reasons, we wish to support htseq-count because it is part of a reference
>>> RNA-seq protocol (http://www.ncbi.nlm.nih.gov/pubmed/23975260), and
>>> because I
>>> haven't gotten around to comparing timing and functionality with
>>> GenomicAlignments.  This is probably in a different thread, but e.g.
>>> is it known
>>> that GenomicAlignments::summarizeOverlaps() produces identical results
>>> to
>>> htseq-count with equivalent parameters?  What about timing?
>>>
>>
>> Perhaps Valerie can chime in with specifics.
>>
>> It is very hard to say that two algorithms are the 'same', in general
>> the functionality of ht-seq and summarizeOverlaps is comparable; both
>> support multiple counting modes (including in the case of
>> summarizeOverlaps user-specified modes) but it would not be completely
>> surprising if there were cases where the behaviour was different.
>>
>> The parathyroidSE vignette
>>
>>
>> http://bioconductor.org/packages/release/data/
>> experiment/html/parathyroidSE.html
>>
>>
>> details use of summarizeOverlaps for counting.
>>
>> The Rsubread manuscript Table 1
>>
>>    http://www.ncbi.nlm.nih.gov/pubmed/24227677
>>
>> contains a performance comparison, although the memory consumption of of
>> summarizeOverlaps as reported in that paper appears to rely on reading
>> an entire file in to memory (files are iterated in chunks when processed
>> in the way described by the parathyroidSE vignette; this should have
>> minimal cost for overall speed but provide more reasonable memory
>> management). Rsubread is not available on Windows.
>>
>> Martin
>>
>>
>>> _Taku
>>>
>>>
>>>
>>> On Thu, Dec 5, 2013 at 5:14 AM, Michael Lawrence
>>> <lawrence.michael@gene.com
>>> <mailto:lawrence.michael@gene.com>> wrote:
>>>
>>>     It would be appreciated to know where the current counting methods
>>> fall
>>>     short; i.e., why htseq-count is necessary.
>>>
>>>     Thanks,
>>>     Michael
>>>
>>>
>>>     On Thu, Dec 5, 2013 at 12:30 AM, Martin Morgan <mtmorgan@fhcrc.org
>>>     <mailto:mtmorgan@fhcrc.org>> wrote:
>>>
>>>         On 12/04/2013 11:17 PM, Taku Tokuyasu wrote:
>>>
>>>             Hello,
>>>
>>>             We are trying to support NGS pipelines with SAM input to
>>>             htseq-count, w/o
>>>             requiring a samtools install.  Has Rsamtools implemented /
>>> planned
>>>             any support
>>>             for BAM to SAM conversion?  I notice this has been
>>> requested before
>>>             (e.g. May
>>>             2012,
>>>
>>> http://comments.gmane.org/__gmane.science.biology.__
>>> informatics.conductor/41344
>>>
>>>
>>> <http://comments.gmane.org/gmane.science.biology.
>>> informatics.conductor/41344>),
>>>
>>>             so
>>>             I was wondering if there were any updates on this.
>>>
>>>
>>>         I added this to Rsamtools 1.15.14; this requires other package
>>>         dependencies to be current. I had delayed adding this because
>>> it seems a
>>>         step backward, to a relatively inefficient representation.
>>>
>>>         Other counting alternatives not requiring coercion to SAM
>>> files are
>>>         GenomicAlignments::__summarizeOverlaps (acting on BamFile /
>>> BamViews /
>>>         GAlignments / GAlignmentPairs, counting bins as GRanges /
>>> GRanges list
>>>         from TxDb or standard GTF etc files via rtracklayer::import) and
>>>         Rsubread::featureCount (SAM or BAM files, built-in or GTF or SAF
>>>         annotation files).
>>>
>>>         Please let me know if there are issues with the implementation.
>>>
>>>         Martin
>>>
>>>
>>>             Regards,
>>>
>>>             _Taku
>>>
>>>             Taku Tokuyasu
>>>             Computational Biology Core
>>>             UCSF Helen Diller Family Comprehensive Cancer Center
>>>
>>>
>>>
>>>
>>>         --
>>>         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 <tel:%28206%29%20667-2793>
>>>
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>>>
>>>
>>>
>>>
>>
>>
>
>

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