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

[Dario Strbenac]

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.

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Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia