Hi,
I'm trying to map a data set containing 454 reads to a reference genome
using LASTZ alignment package in Galaxy. I'm following a workflow used for
Illumina reads with the only change in the alignment package, i'm using
LASTZ instead of bowtie/bwa. The following is the procedure please correct
Is it possible when renaming a dataset in a workflow to have it fill in
the dataset number like the default labels?
For example the default label may be "Filter on data 17". What if I want
it to be "High coverage on data 17"? Could I put some special variable in
the text to tell Galaxy to fi
While this is not currently possible, we have recently discussed exposing extra
fields for use in both parameters and rename actions. If you're interested,
I've created a bitbucket enhancement request
(https://bitbucket.org/galaxy/galaxy-central/issue/623/expose-more-fields-to-rename-action-and
Hello Thomas,
For 454 data, there is a specific screencast that may be of interest. Go
to http://usegalaxy.org and scroll in the middle pane to find quickie #15.
We have had very high usage over the last few days, but have since been
able to clear out more resource. Your job will likely start
Hello William,
The tools in "NGS: QC and manipulation", especially those in the
sub-section "AB-SOLiD data" can do the manipulations needed before
mapping. It may be helpful to view the screencast at
http://usegalaxy.org, center pane, quickie #9.
Hopefully this helps to get you started,
Bes
Hello David,
Generating a consensus fasta sequence from a BAM or Pile-up file is not
yet possible in Galaxy. To date, the Tool Shed also does not have a
wrapped/novel tool for this function either.
If you or another user were to create such a wrapped tool, it would be
most welcome. As would
Jen/ Jeremy/ Galaxy team,
Is there any plan of implementing gene fusion version of TopHat in Galaxy
perhaps in next few months or so? Alternatively, if some one has used with gene
fusion using TopHat in Galaxy frame work please share.
Thanks.
Vasu Punj___
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