Hi Ann,
A pause function that truly stops an alignment job, permits inspection
of intermediate results, then resumes it, is probably not going to be
implemented. But we'll send more feedback about that if I have it incorrect.
The best advice I have to consider running a smaller sample of data
through as a test set. It can be tricky to make truly "representative"
test sets at first pass, but after this run completes, you could
probably identify one by coordinates by choosing all of the sequences
that fit within a certain "slices" of genomic regions that contain
transcript models (or whatever feature you are examining) that are
interesting (or difficult!). Then use that with subsequent runs if you
want to tune parameters and have it run quicker. This is what I usually
do - being sure to include some of the uglier regions. Even if I am
never really able to solve them completely, at least I know what they
will look like in the end. You don't want to train your parameters on
all "ideal" cases. With lower quality data, this might be even more
important since you've got a double challenge to manage - query and
target. But that's real data!
Good luck with your project,
Jen
Galaxy team
On 6/26/13 2:33 PM, Ann Holtz-Morris, M.S. wrote:
Hi,
I read
https://www.google.com/url?q=http://dev.list.galaxyproject.org/Can-t-find-new-pause-resume-functionality-in-Dec-2012-Galaxy-td4657331.html&sa=U&ei=KFzLUaHFCaGcjALSq4GQCw&ved=0CAcQFjAA&client=internal-uds-cse&usg=AFQjCNHSziHrbCCmumvDDUtmAeW9RvLRdg
with interest.
I would also like a Pause function as a toggle on/off so I can stop
look at the data being generated. I'm running a BWA alignment that's
been working now for almost 48 hours. It's a decent sized data set but
it had a very low quality second sequencing read. I've quality trimmed
and length filtered. It ended up being only ~50% of the # of reads in
Read1.
I'd love to be able to pause it and see if the data set is behaving
as expected.
Thanks,
Ann
Ann Holtz-Morris
SRA III
de Jong Laboratory
510-428-3885 x 5715
aholtzmor...@chori.org <mailto:aholtzmor...@chori.org>
Shipping and Mailing Address
Attention: Ann Holtz-Morris
CHORI-BACPAC Resources BLMR Bldg.
747 52^nd St.
Oakland, CA 94609-1809
CONFIDENTIALITY NOTICE: This electronic message is intended to be for the use
only of the named recipient, and may contain information that is confidential
or privileged. If you are not the intended recipient, you are hereby notified
that any disclosure, copying, distribution or use of the contents of this
message is strictly prohibited. If you have received this message in error or
are not the named recipient, please notify us immediately by contacting the
sender at the electronic mail address noted above, and delete and destroy all
copies of this message. Thank you.
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/