M***@tnw.utwente.nl
2008-10-27 16:17:31 UTC
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
***@tnw.utwente.nl
_______________________________________________
Genome maillist - ***@soe.ucsc.edu
http://www.soe.ucsc.edu/mailman/listinfo/genome
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
***@tnw.utwente.nl
_______________________________________________
Genome maillist - ***@soe.ucsc.edu
http://www.soe.ucsc.edu/mailman/listinfo/genome