[Bioc-devel] FlipFlop Ignores Read Strand and Requires Antiquated File Formats

[Wolfgang Huber]

Dear Dario

These all look like legitimate suggestions, and probably the package author has something to say on their substance.

But independent of the specifics here, I think we should also keep in mind that the motivations for package submission vary across the project.
Some contributors really take it on themselves to continuously develop and extend a solution for a particular field of science or technology.
This is great, in particular for users.

Others provide a ‘snapshot’ of their work at a particular point in time (e.g. end of PhD thesis) and make their research reproducible, so that others can build on top of it. This is the same as with research papers, which are also rarely supposed to be the “final word” on something but an important advance.
I think this is also great, for the scientific record, and for other method developers who can start from such a snapshot (if not literally then at least conceptually) and move on to do even greater things.

	Best wishes
	Wolfgang


> On Nov 1, 2016, at 6:00 GMT+1, Dario Strbenac <dstr7320 at uni.sydney.edu.au> wrote:
> 
> Hello,
> 
> The package FlipFlop is made for isoform quantitiation. Why are there no options to specify the RNA-seq read strand ? Otherwise, the method produces incorrect counts where overlapping genes on both strands are being transcribed. Also, the software requires a SAM file as input. This is inefficient, since most mapping results are stored as BAM files. It would be better if FlipFlop made more use of the import and export functions available in Rsamtools. Also, requiring the gene database to be in BED12 format creates more unnecessary work for the user. ENSEMBL and GENCODE both provide GTF and GFF3 files, which can easily be imported into R with functions provided by rtracklayer.
> 
> --------------------------------------
> Dario Strbenac
> University of Sydney
> Camperdown NSW 2050
> Australia
> 
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Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
Genome Biology Unit
European Molecular Biology Laboratory (EMBL)
Heidelberg, Germany

wolfgang.huber at embl.de
http://www.huber.embl.de