We are aware of this new issue with the Firefox 23.0.1 update. Using an
alternate browser is recommended to avoid the problem with direct
https-http connections, as several of Galaxy's Get Data tools/sources
are impacted. Our team is reviewing solutions at a priority.
This message indicates that an error occurred on the cluster node
processing the job. Normally these are not linked to inputs or tools and
the general solution is to re-run the job. Please give this a try today
- it is possible the error was linked to recent transient server issues.
In general, you can use *'**NGS: Picard (beta) - SAM to FASTQ'* to
extract sequences (convert BAM SAM first), but this tool does not add
in extra sequence based off the reference genome (or pad the associated
quality scores, etc.). I don't know of a Galaxy wrapped tool that does
I am trying to add a custom track of a bed file through Galaxy and i keep
getting this error:
- Error line 325149 of
chrM_rCRS not a recognized sequence (note: sequence names are
Please note, this sequence chrM_rCRS does not exist in the human/hg19
genome browser at UCSC. It is not a recognized sequence.
There is a note about this on the gateway page:
See the paragraph titled: Note on chrM
On 9/12/13 1:25 AM,
Hi Jen and other galaxy-users,
I was using Slice BAM tool on Galaxy to get the alignment overlap with the
targeted intervals. After I got the output BAM file, I used flagstat to
get the detailed information of the output BAM file. What I got from
flagstat is as following.
13704486 + 0 in
I am looking for a de novo RNA-seq workflow that uses trinity. Any idea if
there is one available?
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