Forum: Pacific Biosciences
12-09-2014, 11:27 AM
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Replies: 12
Views: 6,344
@rhall Interesting ... I haven't seen this...
@rhall Interesting ... I haven't seen this smrtmake stuff before. I'd note that the default OVLSIZE (20000) for circularize.mk seems large; I'm looking at two circular bacterial genomes (~5Mbp size)...
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Forum: Pacific Biosciences
12-05-2014, 09:49 AM
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Replies: 12
Views: 6,344
@EulnayM I see the same thing with Gepard and...
@EulnayM I see the same thing with Gepard and sprai's check_circularity.pl script. Gepard shows clear ~6kbp overlap (after zooming in on the 5'-end to 3'-end region of the dot plot) with ~100%...
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Forum: Pacific Biosciences
03-18-2013, 02:40 PM
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Replies: 17
Views: 12,210
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Forum: Bioinformatics
12-20-2012, 04:14 PM
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Replies: 1
Views: 1,742
Are you sure the plot is different for aligned...
Are you sure the plot is different for aligned sequence? Wherever you're looking, if you left-click on a location in one or the other sequence, the other sequence(s) will shift to line up with the...
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Forum: Genomic Resequencing
05-18-2012, 01:25 AM
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Replies: 3
Views: 4,791
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Forum: Bioinformatics
05-07-2012, 01:44 PM
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Replies: 4
Views: 2,927
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Forum: Bioinformatics
05-02-2012, 04:25 AM
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Replies: 4
Views: 2,927
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Forum: Bioinformatics
04-11-2012, 02:05 PM
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Replies: 26
Views: 10,552
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Forum: RNA Sequencing
04-10-2012, 01:52 PM
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Replies: 7
Views: 3,870
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Forum: Bioinformatics
04-10-2012, 01:19 PM
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Replies: 5
Views: 4,531
I'm having trouble finding bioinformatics...
I'm having trouble finding bioinformatics protocols for doing this too. The problem seems to be that most tools (scripture, PASA?, IsoInfer, Inchworm, IsoEM, NSMAP, MISO are most of what I've looked...
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Forum: RNA Sequencing
04-10-2012, 01:11 PM
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Replies: 7
Views: 3,870
Are there different read groups, perhaps two...
Are there different read groups, perhaps two different samples in the BAM? How was it produced (tool, command example, etc.)? Maybe you could show examples of SAM lines from each of the two files ...
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Forum: 454 Pyrosequencing
01-23-2012, 03:57 PM
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Replies: 6
Views: 4,359
Can I ask, biocomfun, how you used CORAL to...
Can I ask, biocomfun, how you used CORAL to correct 454 reads using Illumina reads? As far as I can tell, CORAL simply takes a set of reads and does multiple alignment ... i.e. you can't specify a...
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Forum: Bioinformatics
12-02-2011, 10:48 AM
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Replies: 9
Views: 5,947
@slowsmile - can you comment on the p-values /...
@slowsmile - can you comment on the p-values / fold changes, especially in light of @Jon_Keats' post? Do the stats for the original 173 genes (presumably the most obvious DE cases) remain roughly the...
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Forum: Bioinformatics
08-05-2011, 12:32 PM
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Replies: 6
Views: 12,597
Yes, on both counts.
By the way, the...
Yes, on both counts.
By the way, the -exp_cov value is used to determine which parts of the graph are likely due to repeat sequence ... some multiple (maybe 1.5?? I forget...) of the -exp_cov...
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Forum: Bioinformatics
07-20-2011, 11:40 AM
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Replies: 1
Views: 2,272
Hey John! I'm looking for this as well ... did...
Hey John! I'm looking for this as well ... did you ever get an answer from somewhere else? Specifically I think I'm seeing reduced (compared to alignments using bwa-0.5.8?) mapping qualities for...
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Forum: Bioinformatics
06-20-2011, 02:56 PM
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Replies: 292
Views: 160,522
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Forum: Bioinformatics
05-19-2011, 11:03 AM
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Replies: 13
Views: 10,203
Library type / depth issues
Some of the parameters of the data (library insert sizes, depths) are determined more by the parties who are willing to donate novel data "to the cause," rather than pure ab initio considerations of...
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Forum: Bioinformatics
05-18-2011, 11:02 AM
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Replies: 13
Views: 10,203
Linked to Genome10K Project
Hi all,
This was actually a collaborative effort between David Haussler's group at UCSC, Ian Korf's lab here at UC Davis, and the UC Davis Genome Center's Bioinformatics Core. David Haussler...
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Forum: Bioinformatics
05-11-2011, 01:41 PM
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Replies: 19
Views: 140,982
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Forum: Bioinformatics
03-09-2011, 01:05 PM
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Replies: 31
Views: 18,826
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Forum: Bioinformatics
03-09-2011, 12:37 PM
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Replies: 31
Views: 18,826
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Forum: Bioinformatics
03-03-2011, 02:45 PM
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Replies: 31
Views: 18,826
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Forum: Bioinformatics
03-03-2011, 02:07 PM
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Replies: 31
Views: 18,826
We're looking at using Ensembl's Variant Effect...
We're looking at using Ensembl's Variant Effect Predictor right now ... but with a non-model organism (or at least a model organism with some regions replaced by a "better" assembly). It seems like...
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Forum: Bioinformatics
02-08-2011, 12:59 PM
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Replies: 6
Views: 2,440
Thanks Laura! - Ensembl's Variation Effect...
Thanks Laura! - Ensembl's Variation Effect Predictor worked perfectly, and the online version is set up for Aribidopsis and about 8 other plants, so it didn't even require any hacking.
We talked...
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Forum: Bioinformatics
02-04-2011, 01:22 PM
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Replies: 6
Views: 2,440
Thanks!
Thanks krobison, swbarnes,
I checked out your search results link, krobison ...
GAMES and MU2A seem to be limited to human (similarly for SNPnexus, which I just stumbled across), and MU2A is a...
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