User: ebrown1955

gravatar for ebrown1955
ebrown1955300
Reputation:
300
Status:
Trusted
Location:
United States
Last seen:
2 years, 11 months ago
Joined:
4 years, 3 months ago
Email:
a******@gmail.com

Posts by ebrown1955

<prev • 43 results • page 1 of 5 • next >
0
votes
1
answer
1.7k
views
1
answers
Answer: A: Calculate reciprocal overlap for thousands of samples
... You can use bedtools intersect for this. http://bedtools.readthedocs.org/en/latest/ ...
written 3.2 years ago by ebrown1955300
0
votes
0
answers
1.3k
views
0
answers
Comment: C: Tools to view LRR and BAF for Illumina SNP arrays
... By the way. PennCNV does allow this, however I have to input SNP ids, and I just was hoping to input region coordinates instead of SNP ids (I don't have the information readily available) ...
written 3.4 years ago by ebrown1955300
0
votes
0
answers
1.3k
views
0
answers
Tools to view LRR and BAF for Illumina SNP arrays
... Are there any tools (free) that can view BAF and LRR for Illumina SNP array data? I'm trying to visualize specific regions quickly and easily. ...
baf snp array lrr written 3.4 years ago by ebrown1955300 • updated 3.3 years ago by Biostar ♦♦ 20
0
votes
2
answers
1.9k
views
2
answers
Comment: C: How does GATK PhaseByTransmission define the phasing of Father and Mother?
... You can do PhaseByTransmission first, then ReadBackedPhasing with the '-respectPhaseInput' option, which will keep the PhaseByTransmission phases. ...
written 3.4 years ago by ebrown1955300
0
votes
0
answers
1.2k
views
0
answers
Calling inheritance from phased/unphased genotype data
... I'm working on a script that calls inheritance for children in complex families within VCF files. After much thought, I'm a little confused on what to do with phased genotypes. Would these assumptions be correct? Can anyone come up with any special circumstances? If the child is 0|0 and the moth ...
de novo dnaseq phasing inheritance written 3.4 years ago by ebrown1955300
0
votes
0
answers
1.3k
views
0
answers
Comment: C: Calculating bam/fastq metrics
... UPDATEl: I actually used CalculateHSMetrics from the PicardTools suite for percent on target. ...
written 3.4 years ago by ebrown1955300
1
vote
0
answers
1.3k
views
0
answers
Calculating bam/fastq metrics
... Hi All, I just got a few QC questions back from my sequencing center, as they are trying to streamline the sequencing process for our next batch of samples. The questions are: 1) What was the average duplication rate? 2) What was the % On Target ? 3) What was the uniformity of the reads on target? ...
exome sequencing fastq bam written 3.4 years ago by ebrown1955300
4
votes
3
answers
1.7k
views
3
answers
Does anyone know any specific 1000 genomes WGS data that is around 30x coverage?
... I noticed that 1000 genomes data files don't seem to say what the coverage is for each sample, only that some are high coverage and some are low coverage. I know that high coverage can be anywhere between 30 and 50x, however, I'm looking for a sample that is closer to 30x so I can test my processing ...
1000genomes controlsample written 3.4 years ago by ebrown1955300 • updated 3.4 years ago by Vincent Laufer1.0k
0
votes
2
answers
1.6k
views
2
answers
Comment: C: Buying computational resources vs. renting allocation on cluster
... Yeah, good answer. I was thinking about some 1000 genomes data with similar coverage, and run them on one of our current systems at different levels of parallelization, and check how long this would take. I was actually surprised to see a single machine with 100+ threads. This Dell system had 4 ver ...
written 3.4 years ago by ebrown1955300
5
votes
2
answers
1.6k
views
2
answers
Buying computational resources vs. renting allocation on cluster
... My lab is about to receive about WGS (30X) data (fastqs) on about 400-1500 samples (depending on how many we get at a time) that need to be processed and analyzed. We are trying to figure out the best route for computational resources. Here are some options: We can buy an allocation from Google C ...
cluster cloud computing server processing power written 3.4 years ago by ebrown1955300 • updated 3.4 years ago by Brian Bushnell16k

Latest awards to ebrown1955

Student 3.5 years ago, asked a question with at least 3 up-votes. For Running BWA parallel on 1000 samples
Appreciated 3.6 years ago, created a post with more than 5 votes. For A: How to merge VCF files for SNP's ?
Scholar 3.7 years ago, created an answer that has been accepted. For A: How to merge VCF files for SNP's ?
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: How to merge VCF files for SNP's ?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1496 users visited in the last hour