Hello Marije, Could you send me the first 8-10 lines of your wig file so that I can take a look at it? Please send your reply directly to me without cc'ing the whole list.
Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu [EMAIL PROTECTED] wrote: > Dear sir / madame, > > > > I've performed Chromatin Immunoprecipitation and had a service company > sequence the fragments with an Illumina Solexa sequencer. After the > sequence reads had passed the quality check, the ELAND program was used > to align the reads to the hg18 provided by UCSC as part of the Illumina > data analysis pipeline. This was also done by the same company. > > Thereafter the aligned sequence tags were fed into the FindPeaks > 3.1.9.2. package written by the Canada Michael Smith Genome Sciences > Centre in order to 1. analyze the short-read sequences to identify areas > of enrichment of the protein of interest and 2. generating wig files for > use in the UCSC genome browser. The company performed a FindPeaks run > with standard settings. After I adjusted the settings to my own wished, > I performed another FindPeaks run. The wig file that was generated by > the company could be put into the genome browser without any problems. > After uploading the wig file created by myself, it seems at first that > it went all right because the following screen appears: > > > > Manage Custom Tracks > > > > > > > > genome: Human assembly: Mar. 2006 [hg18] > > Name > > Description > > Type > > Doc > > > > test3_duplicates_subpeaks_len_triangle > <http://genome.ucsc.edu/cgi-bin/hgCustom?hgsid=114649973&hgct_table=ct_t > est3duplicatessubpeakslentriangle> > > test3_ht:1.0_FL:triangle_dupe_rds_inc > > wiggle_0 > > > > > > > > > > > > > > > > But when I want to go to the genome browser, I the following error > message appears: > > > > Internal error (Unmatched ' line 1 of input: missing closing ' ): > removing custom tracks > > > > Do you know by any chance what went wrong? I've already tried the > standard FindPeaks settings the company also used, but it doesn't work > form me. > > I hope someone will have an answer for me. Thanks in advance! > > > > Regards, > > Marije > > > > Drs. Marije Telgenkamp, MD > > PhD candidate Molecular Cell Biology > > Department of Science and Technology > > University of Twente > > Building Zuidhorst, room ZH125 > > PO box 217 > > 7500 AE Enschede, The Netherlands > > Phone: +31 (0)53 4893554 > > Fax: +31 (0)53 4891105 > > [EMAIL PROTECTED] > > > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
