Hello,
I'm working on a local instance of Galaxy-dist and I just
updated it. Right after the update I tried to run the
cleanup scripts. Unfortunately what I'm getting is the
following error:
# sh delete_datasets.sh -d 0 -r
Traceback (most recent call last):
File "./scripts/cleanup_datasets/cle
Hi,
I need to sort a BAM file by read names, I was wondering if this is
possible with a tool included in Galaxy?
I know any BAM file produced inside Galaxy will be sorted by
coordinates, but I couldn't find an option to change this to queryname
in any tool. Picard has the tool SortSam[1], perfect
Hello Carlos,
Start by converting your BAM file to SAM, with "NGS: SAM Tools ->
BAM-to-SAM". It is probably best to include the header if you plan to
use the SAM file in downstream tools later on. If not, you can skip the
step where it is saved.
Next, to save back the SAM header into a separ
Hi Rocco,
To help us get oriented, which galaxy-dist pull did you start from and
which did you update to? If you have the release date/hg pull numbers,
that would be great. If you need to reference, these are the prior
distributions:
http://wiki.g2.bx.psu.edu/DevNewsBriefs
Ideally, you would
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