Problems with mapping SOLID color space sequences to hg19 using TopHat

[davidehs]

Hi,

I got a problem when mapping SOLID short sequences to hg19 using tophat. The human UCSC hg19 color space index was downloaded from bowtie website(http://bowtie-bio.sourceforge.net/manual.shtml). The variant, $bowtieInputFile, in the following command, is the name of the fastq file. I have used the same command line, except omiting argument -C (which is specially for color space), to successfully map base space reads to hg19. But the problem, "segment-based junction search failed with err =1", always show up when doing color space mapping at the step "Searching for junctions via segment mapping".

Do you guys have any idea how I can avoid this problem?

Thanks in advance!

David





> tophat --solexa-quals -p 12 -C --output-dir tophat.output ~/Utilities/bowtie/bowtie-0.12.7/indexes/hg19_c $bowtieInputFile | tee -a fastq2bigwig.log

[Fri Jun 24 16:11:08 2011] Beginning TopHat run (v1.3.0)
-----------------------------------------------
[Fri Jun 24 16:11:08 2011] Preparing output location tophat.output/
[Fri Jun 24 16:11:08 2011] Checking for Bowtie index files
[Fri Jun 24 16:11:08 2011] Checking for reference FASTA file
Warning: Could not find FASTA file /home/david/Utilities/bowtie/bowtie-0.12.7/indexes/hg19_c.fa
[Fri Jun 24 16:11:08 2011] Reconstituting reference FASTA file from Bowtie index
Executing: /home/david/bin/bowtie-inspect /home/david/Utilities/bowtie/bowtie-0.12.7/indexes/hg19_c > tophat.output/tmp/hg19_c.fa
[Fri Jun 24 16:13:12 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Fri Jun 24 16:13:12 2011] Checking for Samtools
Samtools Version: 0.1.16
[Fri Jun 24 16:13:12 2011] Generating SAM header for /home/david/Utilities/bowtie/bowtie-0.12.7/indexes/hg19_c
[Fri Jun 24 16:13:13 2011] Preparing reads
format: fastq
quality scale: solexa33 (reads generated with GA pipeline version < 1.3)
Left reads: min. length=51, count=737097
[Fri Jun 24 16:13:26 2011] Mapping left_kept_reads against hg19_c with Bowtie
[Fri Jun 24 16:13:46 2011] Processing bowtie hits
[Fri Jun 24 16:15:16 2011] Mapping left_kept_reads_seg1 against hg19_c with Bowtie (1/2)
[Fri Jun 24 16:16:03 2011] Mapping left_kept_reads_seg2 against hg19_c with Bowtie (2/2)
[Fri Jun 24 16:16:50 2011] Searching for junctions via segment mapping
[FAILED]
Error: segment-based junction search failed with err =1

[jbrwn]

had the same error. you may want to give the new version (Tophat 1.3.1) a try since there were some SOLiD specific fixes in it. if that doesn't work, i've had some luck rolling back to 1.2.0, and, more routinely, use abi's aligner.