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Old 07-27-2009, 08:45 AM   #1
Location: Bethesda, MD

Join Date: Apr 2009
Posts: 51
Default TopHat output and USCS genome browser question

Hi folk! This is my first post and I'm quite new to next-gen sequencing analysis, so please be kind

Here is some background on my data:
mRNA from rat heart tissue was isolated and sequenced using a Heliscope from Helicos. I then converted the sms file generated by Helicos to a fasta file using a script in the Helisphere software. From there I used TopHat to look for splice junctions.

From what I can see, everything went fine. The TopHat output includes all the files that I would expect it to include. Now, when I tried to view the .BED and .WIG files using the UCSC genome browser I have problems.

Using the input found here --> I tried to view my files after selecting genome->rat and the most recent assembly. I try to upload my .BED file and received the following error:
"Error File 'junctions.bed' - Unrecognized format line 2 of custom track: gi|34868215|ref|NW_047355.1|Rn11_WGA1875_4 1124643 1138858 JUNC00000001 2 - 1124643 1138858 255,0,0 2 11,10 0,14205 (note: chrom names are case sensitive)"

I am wondering if I'm even attempting to use the right tool to view the file or if there is some upstream problem?

Any help would be appreciated.

sdarko is offline   Reply With Quote
Old 08-03-2009, 03:50 PM   #2
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Location: Kansas City, MO

Join Date: Aug 2009
Posts: 2

The pre-built index for rat is built from NCBI contigs. In the first column of the bed file where it should be giving you a chromosome name you're getting the contig instead. You can build your own index from the UCSC fasta files with bowtie-build and it won't have this problem.
glh is offline   Reply With Quote

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