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Old 11-17-2010, 03:03 AM   #6
oliviera
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Location: germany

Join Date: Apr 2010
Posts: 31
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I have the same problem with tophat 1.1.3, and do not manage to solve the problem.

I used :
./tophat --solexa1.3-quals --no-novel-juncs -G Danio_rerio.Zv9.60.gtf -o /5cq15 Danio_rerio.Zv9.60 5.fastq

the log file is the same as yours:
prep_reads v1.1.3 (1680)
---------------------------
/home/olivier/src/illumina_software_version/tophat_113/bin/prep_reads: unrecognized option '--gtf-annotations'

Funny thing however in the gtf_juncs log file: seems to do something their
gtf_juncs v1.1.3 (1680)
---------------------------
Extracted 218405 junctions from /Danio_rerio.Zv9.60.gtf

I tried gtf and gff format and both failed.
When I run without -G option it works fine...
Any feedback would be much appreciated

Cheers

Oliviera
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