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Search: Posts Made By: P-Richmond
Forum: Bioinformatics 08-09-2016, 11:24 AM
Replies: 1
Views: 1,131
Posted By P-Richmond
Trio Structural variant genotyping

Hello,
I'm working with trio structural variant calling from Illumina paired-end WGS. I've called variants using LumpySV, and I have both bedpe and vcf files for mother, father, and child.

I...
Forum: Bioinformatics 11-29-2012, 06:14 AM
Replies: 1
Views: 864
Posted By P-Richmond
Assembly

Hello SEQanswers,
We're going to be de novo assembling a genome of an organism with a genome size between 20-50MB. We're looking for recommendations on what types (454, Illumina SIPES, Illumina...
Forum: Bioinformatics 11-01-2012, 10:19 AM
Replies: 0
Views: 1,332
Posted By P-Richmond
Manhattan Plots in R for Gene Expression

I'm trying to visualize gene expression on a genome-wide basis, and I'd like to accomplish this via a Manhattan Plot (part of the R 'gap' package). Does anyone have experience with this? The manual...
Forum: Bioinformatics 10-08-2012, 11:29 AM
Replies: 0
Views: 1,293
Posted By P-Richmond
visualizing strand-specific read coverage per position

Hello,
I'm looking to display strand-specific RNA-seq data coverage data. I currently generate per-position strand specific coverage using genomeCoverageBed (genomeCoverageBed -ibam <in.bam>-d -s...
Forum: Bioinformatics 09-04-2012, 11:35 AM
Replies: 3
Views: 1,462
Posted By P-Richmond
I've written a script that takes a reference...

I've written a script that takes a reference fasta and a corresponding annotation gff3 and calculated for verified ORFs (non-overlapping) the synonymous vs. nonsynonymous percentages. For S288c,...
Forum: Bioinformatics 08-31-2012, 10:52 AM
Replies: 7
Views: 9,057
Posted By P-Richmond
I wholeheartedly agree with aeonsim, and another...

I wholeheartedly agree with aeonsim, and another important factor in the variation calling process at determining true variants lies in the usage of a few different mapping tools. You'd be amazed at...
Forum: Bioinformatics 08-30-2012, 09:41 AM
Replies: 7
Views: 9,057
Posted By P-Richmond
So if GATK claims that their QV scores are PHRED...

So if GATK claims that their QV scores are PHRED then they make some interesting assertions on the % chance that something is wrong, since usually you see phred scores on a reasonable scale (0-40,...
Forum: Bioinformatics 08-30-2012, 08:45 AM
Replies: 3
Views: 1,462
Posted By P-Richmond
Coding/Noncoding and Synonymous/Nonsynonymous

Has anyone calculated, for a given genome (S288c), what the % of the genome is coding vs noncoding? Also, has anyone calculated for the coding regions, the % of positions that when mutated cause a...
Forum: Bioinformatics 08-30-2012, 08:43 AM
Replies: 7
Views: 9,057
Posted By P-Richmond
I don't believe that any "standard" VCF considers...

I don't believe that any "standard" VCF considers the quality to be phred scored. (Samtools isn't, GATK UnifiedGenotyper isn't, Freebayes isn't, VARiD isn't). In my experience the SNP/Indel quality...
Forum: Bioinformatics 08-06-2012, 12:44 PM
Replies: 2
Views: 1,951
Posted By P-Richmond
Genome Assembly

Hello,
I am trying to assemble a genome (estimated at ~28mb) and I have the following types of sequencing data:
454 reads (~3 million reads)
Illumina Single End 50 bp (~45 million reads )...
Forum: Bioinformatics 03-07-2012, 12:21 PM
Replies: 14
Views: 5,044
Posted By P-Richmond
http://getsatisfaction.com/gsa You are in...

http://getsatisfaction.com/gsa

You are in the wrong place for this. Post your error to the above address. However, they will insist that you first download the newest version of GATK since they...
Forum: Bioinformatics 01-12-2012, 01:01 PM
Replies: 5
Views: 4,198
Posted By P-Richmond
Any luck in "cleaning up the data"? I have a...

Any luck in "cleaning up the data"? I have a similar problem, but I'm working in S. cerevisiae and keep running across artifacts of the alignements I'm using (read pairs that map to familial genes...
Forum: Bioinformatics 10-29-2010, 12:54 PM
Replies: 4
Views: 2,850
Posted By P-Richmond
BFast fastq imput

Hello,
I'm new to the use of ColorSpace ABI-SOLiD data (and new to SeqAnswers) and would like to inquire about the use of BFast to map my reads to a genome. I began with mate paired genomic ABI...
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