Thanks Jennifer,
Since I did have an error when I run tophat2 with, as reference, a fasta
from my history, so I modified line 105 of tophat wrapper
(bowtie2-build instead of bowtie-build in command line).
Now "Tophat for Illumina Find splice junctions using RNA-seq data " runs
without error.
Hi Sarah,
On 4/11/13 8:02 AM, Sarah Maman wrote:
Thnaks Jennifer,
Excuse me, my previous mail contains an error : In fact, the reference
genome from my history was a fasta format (the name was GTF file but
the format was fasta...).
So, when I run tophat with a reference genome from your hist
Hi Sarah,
It still sounds like there is a path problem - this is why the tools are
looking in the wrong loc file. When bowtie2/tophat2 installs, it will
create a symbolic link that names itself as just "bowtie" or "tophat",
pointing to the v2 binaries.
When you run these, what do you get?
Thanks a lot Jennifer,
Restart, full paths were OK.
I don't know why but the 2nd version of Tophat (so the tophat tool
available from Galaxy) search indexs in bowtie-index.loc file and not in
bowtie2-index.loc
So, I've added my bowtie2 index paths in bowtie-index. loc file and
tophat run...
Hi Sarah,
Let's try to sort this out. Your problem does not seem to be the same as
in the question referenced, but we can see. First - just to double check
- since setting up the genome, you have restarted the server? If not, do
that first and check to see if that fixes the problem. Basically,
Hello,
When I run tophat ("Tophat for Illumina Find splice junctions using
RNA-seq data ), the job failed with truncated files. However, index
files are available and I get exactly the same error message using
built-in index or one of my history.
/
Tool execution generated the following err
