Hi Michael -- I'll respond off-list; this level of detail is really internal to the package. Martin
Michael Muratet wrote: > Greetings > > The latest version of the Illumina SCS software (v2.4) writes intensity > files to network disk storage in separate folders for each cycle and > without leading zeros, e.g., s_1_10.cif. The position files, however, do > have leading zeros, e.g., s_1_0010_pos.txt. I checked the manuals and > couldn't find a way to change one file name or the other and so I > checked with Illumina and their response is below. > > I think the best way to handle the difference WRT reading *.cif files in > ShortRead is to make a list of all pos file names, delete the leading > zeros, and then search that list with the pattern from readIntensities. > Does that sound reasonable? > > Cheers > > Mike > > Begin forwarded message: > >> From: Tiffany Briere <[email protected]> >> Date: October 9, 2009 10:08:25 AM CDT >> To: "[email protected]" <[email protected]> >> Subject: RE: SFC#00118080 - Control over file name format? >> Reply-To: [email protected] >> >> Dear Mike, >> >> As I promised, I checked with one of our bioinformaticists. The >> naming of intensity files is not controllable through a config setting. >> >> Please contact me through [email protected] if you have any >> additional questions. >> >> Best regards, >> Tiffany >> >> Tiffany Briere >> Assoc Technical Applications Scientist >> Illumina, Inc. >> 9885 Towne Centre Drive >> San Diego, CA 92121-1975 >> Tel: 800-809-4566 >> Fax: 858-202-4766 >> E-mail: [email protected] >> Web: www.illumina.com >> >> >> -----<Email Received>----- >> From: [email protected] >> Sent: 10/08/2009 07:47 AM PDT >> To: [email protected] >> CC: >> Subject: Control over file name format? >> >> Greetings >> >> I have heard that the user has some control over the intensity file >> names (*.cif/*.nse) via a XML config file. It would be great if we >> could get the 'old' style name that has leading zeros rather than, for >> example, s_1_10.cif. I can't find anything in the manuals. Is this >> true? How do you go about it? >> >> 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 > > 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 > > > > > -- 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
