Forum: Illumina/Solexa
06-05-2014, 09:25 AM
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Replies: 3
Views: 3,285
Next-generation tutorial
Hi everyone!
I am a new biochemistry graduate student. I have started working with next-generation sequencing. During my undergraduate studies, I learned the Sanger method very well but not the...
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Forum: Bioinformatics
03-04-2014, 11:40 AM
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Replies: 0
Views: 1,079
Problem retrieving snps and indels from FVB mouse
Hi everyone!
I am looking at co-occurring events in transgenic FVB mice tumours. First, I need to filter out snps and indels. I was reading the following paper: Sequencing and characterization of...
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Forum: Bioinformatics
01-08-2013, 09:51 AM
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Replies: 0
Views: 1,101
PhyloP P-value precision
Hi everyone!
I am using PhyloP to compute p-values. I was wondering if anyone knew how to change the precision (i.e. give me 10 digits instead of 6)?
Thank you!
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Forum: Bioinformatics
12-21-2012, 12:30 PM
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Replies: 0
Views: 1,993
PhyloP or PhastCons
Hi everyone!
I am trying to get p-values for a region in a bed file with PhyloP.
The p-value is reported with 5 decimals (i.e. 0.00000).
Is there a way to change the output? For example, if...
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Forum: Bioinformatics
12-17-2012, 09:43 AM
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Replies: 1
Views: 2,716
phyloP or PhastCons
Hi everyone,
I am looking at phylogeny between 9 plant genomes. I want to look at the conservation of certain elements. I know phyloP and PhastCons are useful tools. However, which one would you...
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Forum: Bioinformatics
12-17-2012, 09:38 AM
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Replies: 4
Views: 7,204
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Forum: Bioinformatics
12-13-2012, 11:49 AM
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Replies: 0
Views: 1,348
PhyloP LRT help
Hi everyone,
I am currently using phyloP LRT scores to look for conserved elements in plants. LRT = Likelihood Ratio Test. I want to find a way to rank conserved elements of different sizes. I...
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Forum: General
12-12-2012, 10:31 AM
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Replies: 1
Views: 1,911
sequencing depth/coverage
Hi everyone!
I am currently looking at cDNA expression. However, I don't understand the concept of depth/coverage. Some people say that it is how many times a nucleotide is sequenced. I thought...
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Forum: Bioinformatics
12-10-2012, 01:49 PM
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Replies: 2
Views: 1,045
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Forum: Bioinformatics
12-10-2012, 12:23 PM
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Replies: 2
Views: 1,045
How to index a genome for BLAST
Hi everyone!
I have just installed BLAST+ 2.2.27 on my mac. I want to run some cDNAs against arabidopsis thaliana's genome. I know I need to download the genome and format it for BLAST searches...
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