Forum: Bioinformatics
09-01-2015, 03:00 PM
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Replies: 1
Views: 1,525
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Forum: Bioinformatics
05-20-2015, 05:41 PM
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Replies: 0
Views: 1,209
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Forum: Bioinformatics
01-08-2015, 06:45 PM
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Replies: 4
Views: 2,216
Thanks Genomax.
Trimmomatic is part of...
Thanks Genomax.
Trimmomatic is part of Trinity, but I am thinking about moving it in a separate directory. I will look into the rest, but is STAR an unusual aligners after BWA? Do I need to keep...
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Forum: Bioinformatics
01-08-2015, 12:13 PM
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Replies: 4
Views: 2,216
Pandora's Toolbox
Hello,
I am developing a toolbox with collection of source codes of efficient bioinformatics programs.
They are available under the condition that you cite the individual authors and not...
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Forum: Oxford Nanopore
09-26-2014, 12:23 PM
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Replies: 47
Views: 19,560
ten fold compared to what?
Check page 13 of...
ten fold compared to what?
Check page 13 of Michael Schatz's slides I posted here.
http://www.homolog.us/blogs/blog/2014/09/26/nanopore-truth-and-nothing-but-the-truth/
Illumina alone - ...
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Forum: Oxford Nanopore
09-26-2014, 10:14 AM
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Replies: 47
Views: 19,560
That is possibly due to the molecule moving...
That is possibly due to the molecule moving through the pore at different speed, and the HMM (Viterbi) calculation for base-calling being fixed at one mode and miscalling in the other mode.
This...
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Forum: Oxford Nanopore
09-26-2014, 10:09 AM
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Replies: 47
Views: 19,560
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Forum: Bioinformatics
08-21-2014, 08:39 PM
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Replies: 5
Views: 2,116
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Forum: General
04-11-2014, 04:30 PM
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Replies: 17
Views: 6,871
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Forum: General
04-11-2014, 03:35 PM
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Replies: 17
Views: 6,871
In the version I worked on two years back for...
In the version I worked on two years back for trying to assemble a large genome (~600MB size), the paired reads needed to be merged into one file.
FASTA Line 1-2 (read1 left)
FASTA Line 3-4...
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Forum: General
04-11-2014, 03:33 PM
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Replies: 17
Views: 6,871
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Forum: Introductions
03-27-2014, 07:54 AM
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Replies: 6
Views: 2,378
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Forum: Bioinformatics
11-25-2013, 10:37 AM
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Replies: 1
Views: 15,864
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Forum: General
10-14-2013, 10:56 AM
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Replies: 6
Views: 3,553
some thoughts -
...
some thoughts -
http://www.homolog.us/blogs/blog/2013/10/14/us-science-funding-let-us/
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Forum: General
10-14-2013, 10:55 AM
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Replies: 6
Views: 5,499
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Forum: General
10-05-2013, 10:34 PM
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Replies: 6
Views: 3,553
You are asking that question in 2013? That is...
You are asking that question in 2013? That is five f***ing years too late.
Look, US financial system went insolvent in 2008. The proper solution would have been to send the bankster crooks to...
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Forum: General
10-05-2013, 08:05 AM
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Replies: 6
Views: 5,499
Pacbio - What is the Typical Throughput?
Based on sparsity of pacbio-related posts, I presume nobody uses the technology. I was at their recent user group meeting and liked the smell of the coffee :)
...
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Forum: General
10-05-2013, 07:48 AM
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Replies: 6
Views: 3,553
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Forum: Bioinformatics
08-25-2013, 07:32 AM
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Replies: 6
Views: 4,467
My first guess (based on seeing your...
My first guess (based on seeing your histograms-k29 chart):
Your coverage is very high and that is making the assembler believe that some noisy k-mers are real. One way to check whether that is...
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Forum: Bioinformatics
07-30-2013, 07:26 PM
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Replies: 4
Views: 1,751
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Forum: Bioinformatics
07-29-2013, 10:32 PM
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Replies: 4
Views: 1,751
Hello,
Seems like an interesting problem....
Hello,
Seems like an interesting problem. Here is what you need to do.
(i) Please draw a k-mer distribution of the Illumina reads. I think your Illumina coverage (30) is slightly on the lower...
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Forum: General
06-26-2013, 05:08 PM
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Replies: 1
Views: 1,792
PacBio tutorials
I am developing a set of simple tutorials on PacBio-related algorithms. Please feel free to give your critical input.
http://www.homolog.us/Tutorials/index.php?p=1.1&s=5
Main blog post is here...
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Forum: Bioinformatics
05-21-2013, 08:34 PM
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Replies: 8
Views: 10,617
Here are the links.
...
Here are the links.
http://www.homolog.us/blogs/blog/2013/05/07/genome-assembly-programs-what-hash-functions-do-they-use/
...
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Forum: Bioinformatics
05-20-2013, 11:17 AM
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Replies: 8
Views: 10,617
I would say GPU is a no-go for genome assembly....
I would say GPU is a no-go for genome assembly. We looked at various options for doing genome assembly in GPUs last year, and could not make the algorithms scale well. Genome assembly programs need...
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Forum: Bioinformatics
04-10-2013, 05:51 PM
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Replies: 18
Views: 32,568
Lizhenyu from BGI explained where I made the...
Lizhenyu from BGI explained where I made the error in thinking. When a read has 100 nucleotides and is split into 21-mers, the read will produce only 80 k-mers, not 100. Here is his full response,...
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