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Forum: Illumina/Solexa 06-05-2014, 09:25 AM
Replies: 3
Views: 3,069
Posted By Avro1986
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...
Forum: Bioinformatics 03-04-2014, 11:40 AM
Replies: 0
Views: 1,052
Posted By Avro1986
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...
Forum: Bioinformatics 01-08-2013, 09:51 AM
Replies: 0
Views: 1,075
Posted By Avro1986
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!
Forum: Bioinformatics 12-21-2012, 12:30 PM
Replies: 0
Views: 1,942
Posted By Avro1986
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...
Forum: Bioinformatics 12-17-2012, 09:43 AM
Replies: 1
Views: 2,683
Posted By Avro1986
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...
Forum: Bioinformatics 12-17-2012, 09:38 AM
Replies: 4
Views: 7,027
Posted By Avro1986
Convert maf (multiple alignment file) to FASTA

Hi everyone,

I have aligned 9 genomes into a maf file. Now, I am trying to convert it into a FASTA file. Does anyone know how?

Thank you!
Forum: Bioinformatics 12-13-2012, 11:49 AM
Replies: 0
Views: 1,320
Posted By Avro1986
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...
Forum: General 12-12-2012, 10:31 AM
Replies: 1
Views: 1,854
Posted By Avro1986
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...
Forum: Bioinformatics 12-10-2012, 01:49 PM
Replies: 2
Views: 1,005
Posted By Avro1986
Thank you!

Thank you!
Forum: Bioinformatics 12-10-2012, 12:23 PM
Replies: 2
Views: 1,005
Posted By Avro1986
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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