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,
On 6/26/13 2:33 PM, Ann Holtz-Morris, M.S. wrote:
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
I'd love to be able to pause it and see if the data set is behaving
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