[Bioc-devel] readGAlignments Lacks strandMode

[Hervé Pagès]

On 01/13/2017 12:36 PM, Hervé Pagès wrote:
> Hi,
>
> No ifelse() statement needed. Just use invertStrand() on your
> GAlignments object to invert its strand.
>
> strandMode is specific to paired-end reads and the supported modes
> reflect what other software do with paired-end reads (e.g. TopHat,
> Rsubread, etc..). These modes don't make sense for single-end reads.
>
> Furthermore note that the mode only affects the way the strand() getter
> for GAlignmentPairs objects combines the strands from the first and last
> end to return a single value for each pair. It does NOT modify the
> strand of each end:
>
>   library(GenomicAlignments)
>   bamfile <- system.file("extdata", "ex1.bam", package="Rsamtools")
>
>   ## strandMode 1
>   galp <- readGAlignmentPairs(bamfile, strandMode=1)[c(1:3, 1572)]
>   as.character(strand(first(galp)))
>   # [1] "+" "+" "+" "-"
>   as.character(strand(last(galp)))
>   # [1] "-" "-" "-" "+"
>   as.character(strand(galp))
>   # [1] "+" "+" "+" "-"
>
>   ## strandMode 2
>   galp <- readGAlignmentPairs(bamfile, strandMode=2)[c(1:3, 1572)]
>   as.character(strand(first(galp)))  # same as with strandMode 1
>   # [1] "+" "+" "+" "-"
>   as.character(strand(last(galp)))   # same as with strandMode 2
I meant  . . . . . . . . . . . . . .   # same as with strandMode 1

H.

>   # [1] "-" "-" "-" "+"
>   as.character(strand(galp))
>   # [1] "-" "-" "-" "+"
>
> As you can see, in both case the strand of the first and last end is
> what's in the BAM file.
>
> I'm a big fan of consistency but generally speaking I don't think
> consistency means that every import function should provide the exact
> same interface, whatever the data to import is. That's why we have
> different functions for different data in the 1st place.
>
> H.
>
> On 01/05/2017 11:00 PM, Dario Strbenac wrote:
>> Good day,
>>
>> readGAlignmentPairs has strandMode but readGAlignments doesn't, which
>> means that single-end strand-specific RNA-seq that generates sequences
>> on the opposite strand to the gene needs a subsequent ifelse
>> statement. The API could be more consistent by providing a strandMode
>> option for readGAlignments and other similar functions in
>> GenomicAlignments.
>>
>> --------------------------------------
>> Dario Strbenac
>> University of Sydney
>> Camperdown NSW 2050
>> Australia
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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