Pause Function Please

Question: Pause Function Please

5.4 years ago by

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 <https: www.google.com="" url?q="<a href=" http:="" dev.list.galaxyproject.org="" Can-t"="" rel="nofollow">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"> &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 aholtzmorris@chori.org Shipping and Mailing Address Attention: Ann Holtz-Morris CHORI-BACPAC Resources BLMR Bldg. 747 52nd 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.

bwa alignment • 892 views

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modified 5.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.4 years ago by Ann Holtz-Morris, M.S. • 80

5.4 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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 -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

ADD COMMENT • link written 5.4 years ago by Jennifer Hillman Jackson ♦ 25k

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