Hi Nicolas -- These sounds like very useful additions, and I'll try to incorporate over the next day or so.
Thank you very much for the contribution! Martin On 02/24/2010 02:55 AM, Nicolas Delhomme wrote: > Hi Martin, everyone, > > I've been looking forward to doing it for a long time now, and, > finally, I got the time. So, I dove into the ShortRead C code to add > some functionalities when loading Illumina export files. I've added an > option to the readAligned method, specifically for the type > "SolexaExport" that will in addition to the default information, > retrieve the multiplex barcode and the paired read number (the 6 and 7th > column of the export file, that were ignored so far). Additionally, > using this option will create the sequence identifier (i.e. the one you > get in a fastq file extracted from an export file) and populate the id > slot of the alignedRead object. > > I've attached the diff of my local working copy with the revision 44842 > of ShortRead (the current one, as of this morning), two example export > files (one from a single-end (SE) and one from a paired-end (PE) > sequencing experiment) and a small R script showing the modified usage. > > I think that these functionalities are very interesting for people, like > me, who have to analyze PE, multiplexed data, and I'd be glad if they > got integrated. > > Finally, I'm, by far, not a C expert, so you might wish/(need?) to > optimize what I've written. > > Best, > > --------------------------------------------------------------- > Nicolas Delhomme > > High Throughput Functional Genomics Center > > European Molecular Biology Laboratory > > Tel: +49 6221 387 8426 > Email: [email protected] > Meyerhofstrasse 1 - Postfach 10.2209 > 69102 Heidelberg, Germany > --------------------------------------------------------------- > > > > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- Martin Morgan 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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
