Hello Dr. Telgenkamp, Your posting was forwarded to me by a colleague, and I felt it would be appropriate to reply to it, despite not being a regular user of this mailing list, as I currently maintain and develop the FindPeaks software package.
I have seen the problem you're describing before, and it appears to have a relatively simple solution - modifying the track line of the wig file will correct the problem, though it may not be simple for all users depending on what software you have available to you. In the past, the solution has been as simple as moving the 'type="wiggle_0"' to follow immediately after word 'track'. The problem seems to arise because FindPeaks 3.1.9.2 produces wig files with the "track" line parameters in a different order from that given in the wig file documentation, (http://genome.ucsc.edu/goldenPath/help/wiggle.html). I don't know why only some files produce the error, through re-ordering the parameters does seem to resolve the issue for the two examples I've seen. This problem has been fixed in FindPeaks 3.2, but was not back ported to FindPeaks 3.1. Unfortunately, FindPeaks 3.2 won't be available as a recompiled jar file for another week or so. In any case, if you'd like to send me your wig file (or just the first 10 lines, either should work, if the file isn't too big), I would be happy to help you find a fix for the problem. Finally, it was also pointed out to me by my colleague that you seem to be using a parameter "-minimum 1". You may wish to raise this value for tracks submitted to the UCSC browser, as this can cause wig files to become very large, and I understand the UCSC browser may not load wig files over 300k long. (Peak heights below 2 are rarely informative anyhow, and significantly add to the size of the file.) Alternately, you might wish to leave this particular parameter off entirely, as a minimum peak height of 1 will still provide all peaks under most circumstances. In any case, feel free to contact me if you need any further help with this issue. There is also a FindPeaks mailing list at [EMAIL PROTECTED], which can be used for any other FindPeaks problems you may encounter in the future. Cheers, Anthony Fejes, BC Genome Sciences Centre Another Email contained: > 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
