Hello,
I was trying to run tophat v1.3.2 on SOLID data and I have this error:
zohra@bart:~/Bureau/cancer$ tophat -o /tmp/tophat_SRR036752/ -g 1 -p 4 -C /home/zohra/indexes_bowtie/humain_ SRR036752.fastq
[Tue Oct 11 13:23:53 2011] Beginning TopHat run (v1.3.2)
-----------------------------------------------
[Tue Oct 11 13:23:53 2011] Preparing output location /tmp/tophat_SRR036752//
[Tue Oct 11 13:23:53 2011] Checking for Bowtie index files
[Tue Oct 11 13:23:53 2011] Checking for reference FASTA file
[Tue Oct 11 13:23:53 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Tue Oct 11 13:23:53 2011] Checking for Samtools
Samtools Version: 0.1.18
[Tue Oct 11 13:23:53 2011] Generating SAM header for /home/zohra/indexes_bowtie/humain_
[Tue Oct 11 13:23:55 2011] Preparing reads
format: fastq
quality scale: phred33 (default)
[FAILED]
Error running 'prep_reads'
Error: qual length (51) differs from seq length (51) for fastq record !
Can you help me.
Thanks
Zohra Saci