Forum: Illumina/Solexa
01-28-2014, 09:27 AM
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Replies: 10
Views: 6,142
Well, once again it depends. Sure, V3/V4...
Well, once again it depends. Sure, V3/V4 sequencing will allow you to ID the microbial community to the level of family (Maybe genus), which given enough samples and experimental variables would...
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Forum: Illumina/Solexa
01-28-2014, 06:50 AM
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Replies: 10
Views: 6,142
1. How much depth is sample dependent. Do you...
1. How much depth is sample dependent. Do you have a hypothesis as to the diversity of the environment? Do you have a question/hypothesis that can be tested with more/less depth? 3 million reads per...
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Forum: Metagenomics
01-20-2014, 03:40 PM
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Replies: 8
Views: 15,419
You know there is a pre-existing way to have...
You know there is a pre-existing way to have multiple runs of 454, Illumina...whatever... within QIIME, right? Just add -n some integer to the split_libraries.py or split_libraries_fastq.py that...
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Forum: Bioinformatics
01-15-2014, 02:53 PM
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Replies: 8
Views: 3,330
Give it a shot- I've never had issues with...
Give it a shot- I've never had issues with App-Deploy before. The last script executed is the activation of the qiime-1.8.0-release/ directory, so if there are any other failures prior, you'll still...
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Forum: Bioinformatics
01-15-2014, 06:49 AM
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Replies: 8
Views: 3,330
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Forum: Bioinformatics
01-15-2014, 06:32 AM
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Replies: 8
Views: 3,330
Have you tried QIIME-Deploy?...
Have you tried QIIME-Deploy? https://github.com/qiime/qiime-deploy
Relatively simple way to upgrade/install QIIME on any Linux box.
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Forum: Sample Prep / Library Generation
11-02-2013, 08:06 AM
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Replies: 4
Views: 9,316
The instrument also lets you "calculate stock...
The instrument also lets you "calculate stock concentration" for each sample. Just click the "Calculate Stock Concentration" button after reading a sample, set the units to ng/uL (Or whatever else...
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Forum: Sample Prep / Library Generation
11-02-2013, 07:20 AM
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Replies: 4
Views: 9,316
Well, from the Life Tech website...
The BR...
Well, from the Life Tech website...
The BR kit has a range of 100pg/uL to 1000ng/uL and the HS has a range of 10pg/uL to 100ng/uL. If you're on the extreme of the BR kit (Sample is 0.150 ish...
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Forum: The Pipeline
10-18-2013, 11:37 AM
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Replies: 80
Views: 240,323
I'm guessing
A) 100%
B) 75/25. Either...
I'm guessing
A) 100%
B) 75/25. Either they release something, or risk losing funding from investors at this point. My bet is that they release the Minion sooner than the Gridion.
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Forum: Illumina/Solexa
10-09-2013, 02:03 PM
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Replies: 5
Views: 2,762
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Forum: Sample Prep / Library Generation
10-02-2013, 12:50 PM
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Replies: 1
Views: 1,047
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Forum: General
09-13-2013, 08:43 AM
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Replies: 0
Views: 2,365
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Forum: Metagenomics
09-06-2013, 08:49 AM
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Replies: 1
Views: 2,728
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Forum: Illumina/Solexa
08-20-2013, 07:17 AM
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Replies: 26
Views: 16,897
I'd love to see the Qscore plot on that run....
I'd love to see the Qscore plot on that run. Excited for amplicon sequencing to see it move out to 2x300. Anyone know the expected release date for said kit (Though I guess that was the question of...
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Forum: Metagenomics
08-14-2013, 07:08 AM
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Replies: 9
Views: 7,212
Honestly? Fermentas Taq. Nothing special- when...
Honestly? Fermentas Taq. Nothing special- when you think about it you're generating a 300-500bp fragment, and the likelihood of a misincorporation is low enough that I can live with it. It works well...
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Forum: Pacific Biosciences
08-07-2013, 05:08 AM
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Replies: 3
Views: 3,650
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Forum: RNA Sequencing
05-11-2013, 11:16 AM
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Replies: 5
Views: 2,756
Trying again, converted my sorted.bam to a...
Trying again, converted my sorted.bam to a sorted.sam and had this error crop up.
Warning: Read D3NH4HQ1:160:C1UJ8ACXX:7:1111:18163:68474 claims to have an aligned mate which could not be found....
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Forum: RNA Sequencing
05-11-2013, 08:41 AM
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Replies: 5
Views: 2,756
That did the trick.
New problem...
...
That did the trick.
New problem...
Warning: No features of type 'exon' found.
Warning: Malformed SAM line: MRNM != '*' although flag bit &0x0008 set
Warning: Malformed SAM line: RNAME != '*'...
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Forum: RNA Sequencing
05-11-2013, 08:22 AM
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Replies: 5
Views: 2,756
HT-Seq Count (Banging Head Against Wall)
So I've seen this error crop up in the forums several times, but attempting to solve with the suggestions (find/replace within the gff file, use the -i option) doesn't seem to help...
When I run ...
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Forum: Metagenomics
03-26-2013, 08:36 PM
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Replies: 4
Views: 5,837
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Forum: Vendor Forum
03-05-2013, 07:54 AM
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Replies: 5
Views: 5,105
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Forum: Illumina/Solexa
02-22-2013, 04:44 PM
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Replies: 1
Views: 1,756
One I'd ask what primer set you used, and what...
One I'd ask what primer set you used, and what hypervariable regions you cross. You could artificially insert NNNNNNN between the reads (A bad idea in my opinion), though really you might be just as...
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Forum: Illumina/Solexa
02-18-2013, 02:37 PM
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Replies: 32
Views: 20,044
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Forum: Illumina/Solexa
01-25-2013, 09:10 AM
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Replies: 11
Views: 4,291
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Forum: De novo discovery
01-25-2013, 07:04 AM
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Replies: 8
Views: 9,422
We run our analyses on a 334 node Intel cluster...
We run our analyses on a 334 node Intel cluster (2x Xeon E5@ 2.0 GHz with 32 GB RAM per node)- I usually call 10 nodes at a time, though I work with bacterial genomes...it takes around 15 minutes to...
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