Michael Muratet wrote: > Greetings > > I would like to be able to use the ShortRead package on CIF file data > from the latest version of the Illumina SCS/Pipeline tools. It appears > that the current version of ShortRead (1.2.1?) doesn't handle this > format. I have a snippet of a R script that will read these binary files > and produce the same output as the Illumina cifToTxt tool and I'm > willing to do the work to incorporate it into ShortRead. Are there > already plans to do this? Can anyone point me to document that describes > the basic syntax and data structures behind R objects of this class? > I've looked at the ShortRead source and I'm not sure I could figure it > out just from that.
Hi Michael -- No, ShortRead does not parse CIF format. Is there a specification somewhere? If you'd like to contribute the relevant parser, that would be great! You'll probably want to use the development version of R and of ShortRead (currently 1.3.33). You're aiming for an object of class AlignedRead, which you would construct from the bits you parse with a call to AlignedRead(<your stuff here>) there is some 'essential' information, like the reads and their quality scores, the chromosome and position of alignement; other stuff gets put in an 'AlignedDataFrame'. See ?AlignedRead and ?"AlignedRead-class" for more. I'm happy to provide additional guidance, too. Martin > > Hopefully, the CIF format will be around for awhile. > > Thanks > > Mike > > Michael Muratet, Ph.D. > Senior Scientist > HudsonAlpha Institute for Biotechnology > [email protected] > (256) 327-0473 (p) > (256) 327-0966 (f) > > Room 4005 > 601 Genome Way > Huntsville, Alabama 35806 > > > > > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
