Just to provide an update to this problem, it seems my initial suggestion was incorrect. The UCSC browser does not like the header lines at the top of the wig file. Removing all of the lines before the one that starts with "track" will correct the problem.
I'm still not certain why this only affects certain files and not others. It may have to do with the line termination character in the header, which I'll ensure is not platform dependent in FindPeaks 3.2. Anthony > > Message: 5 > Date: Mon, 27 Oct 2008 17:17:31 +0100 > From: <[EMAIL PROTECTED]> > Subject: [Genome] ChIP-seq > To: <[email protected]> > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="us-ascii" > > 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
