Forum: Oxford Nanopore
12-01-2015, 09:21 AM
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Replies: 6
Views: 3,323
Interesting, I tried the combined PBcR MHAP...
Interesting, I tried the combined PBcR MHAP pipeline with the oxford.spec and arrived at an assembly in 20 minutes with 98% match to the NCBI ref seq for Lambda.
The DALIGNER, POA and RunCA with...
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Forum: Oxford Nanopore
11-25-2015, 04:55 AM
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Replies: 6
Views: 3,323
Nanocorrect (daligner + poa), is the step...
Nanocorrect (daligner + poa), is the step preceding the celera assembly and nanopolish. This is to say, PBcR and nanopolish are next once the POA is done... When it gets done.
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Forum: Oxford Nanopore
11-24-2015, 05:49 PM
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Replies: 6
Views: 3,323
Partial Order Alignment Step
I'm running through Jared and Nick's Nature Methods de novo assembly approach on my Lambda burn-in FAST5 data. Just to get the pipeline up and running and some familiarity using a focused data set....
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Forum: Illumina/Solexa
03-13-2015, 05:18 AM
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Replies: 1
Views: 1,075
Depending on the type of library preparation...
Depending on the type of library preparation method you use, it could be heterodimers between non-complementary templates within your sample preparation. These heterodimers have complementarity on...
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Forum: Ion Torrent
03-10-2015, 08:44 AM
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Replies: 2
Views: 2,912
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Forum: Illumina/Solexa
03-04-2015, 05:09 AM
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Replies: 13
Views: 3,601
1 in a million cross-overs. The incidence of...
1 in a million cross-overs. The incidence of having one of the indexes cross-over a mispair with another index/barcode is ~1:1000 (if done optimally). The error rate is multiplicative for the dual...
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Forum: Illumina/Solexa
03-03-2015, 05:10 AM
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Replies: 13
Views: 3,601
Just as a follow up to the above posts. It is...
Just as a follow up to the above posts. It is certainly easy enough to dual index with single end read (just needs to be long enough to reach the other end and input the barcode). The downside to...
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Forum: Illumina/Solexa
03-01-2015, 05:11 AM
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Replies: 13
Views: 3,601
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Forum: Illumina/Solexa
02-25-2015, 09:47 AM
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Replies: 5
Views: 2,303
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Forum: Illumina/Solexa
10-14-2014, 09:04 AM
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Replies: 2
Views: 1,360
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Forum: Ion Torrent
07-28-2014, 01:16 PM
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Replies: 1
Views: 1,557
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Forum: Illumina/Solexa
06-04-2014, 10:19 AM
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Replies: 2
Views: 3,984
This is indeed concerning. We synthesized our...
This is indeed concerning. We synthesized our in-line barcoding reagents to have the first 4 bases be randomized followed by our less complex sequences.
Let us all know if you have any issues...
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Forum: Illumina/Solexa
06-02-2014, 10:11 PM
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Replies: 14
Views: 5,671
http://m.pnas.org/content/111/5/1891.full
...
http://m.pnas.org/content/111/5/1891.full
See above. Careful what you assume is a "duplicate."
There are fragmentation and ligation hotspots that may mimic duplicate reads of an amplified...
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Forum: Illumina/Solexa
04-15-2014, 07:13 PM
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Replies: 58
Views: 42,439
Hi Kristen,
Some time back you stumbled...
Hi Kristen,
Some time back you stumbled across our paper on targeted RNA seq: http://seqanswers.com/forums/showthread.php?t=35379
The use of the competitive internal standard molecules...
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Forum: Illumina/Solexa
02-21-2014, 10:45 AM
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Replies: 3
Views: 1,464
Post-PCR cleanup of multiplex amplicon library...
Post-PCR cleanup of multiplex amplicon library prep is almost a given. Ampure beads, gel electrophoresis and band cut out, column exclusions, etc, are all decent options for Illumina library prep...
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Forum: Illumina/Solexa
02-07-2014, 08:39 AM
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Replies: 6
Views: 3,218
The issue with not having biological/library...
The issue with not having biological/library replicates, aside, yes, you can trim the 3' 100 bases from your reads to achieve a pseudo-50 base read length.
I've done this for comparison purposes...
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Forum: Ion Torrent
01-29-2014, 09:19 AM
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Replies: 14
Views: 7,511
Heterodimerization is the primary cause of...
Heterodimerization is the primary cause of polyclonal bead population. Which is to say denaturation of complementary homodimer DNA strands, and subsequent reannealing with a somewhat complementary,...
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Forum: Ion Torrent
12-12-2013, 08:04 AM
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Replies: 6
Views: 6,586
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Forum: Illumina/Solexa
11-29-2013, 01:46 PM
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Replies: 2
Views: 4,639
QIIME pipeline a subset of your reads. A few...
QIIME pipeline a subset of your reads. A few "OTU" consensus sequences will come from this. Blast then against the NCBI nucleotide database and you'll have a general idea if it's technical...
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Forum: Literature Watch
11-26-2013, 01:48 PM
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Replies: 3
Views: 5,863
As to comment on why we moved away from...
As to comment on why we moved away from traditional RNA-seq. Some preliminary data from colleagues using unsupervised biomarker identification in RNA seq libraries from different clinical samples...
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Forum: Literature Watch
11-26-2013, 01:38 PM
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Replies: 3
Views: 5,863
Hi Kristen,
You are correct in your...
Hi Kristen,
You are correct in your statement that we can provide back either median normalized abundance, reference gene normalized abundance, or absolute copies based on the internal standard...
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Forum: Ion Torrent
11-14-2013, 07:20 AM
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Replies: 14
Views: 7,511
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Forum: Literature Watch
11-13-2013, 05:28 PM
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Replies: 3
Views: 5,863
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Forum: Illumina/Solexa
10-15-2013, 01:02 PM
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Replies: 2
Views: 2,374
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Forum: Illumina/Solexa
10-15-2013, 12:55 PM
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Replies: 12
Views: 6,629
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