User: Raygozak

gravatar for Raygozak
Raygozak1.3k
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Location:
State College, PA, Penn State
Website:
http://raygozalab.org/
Last seen:
1 week, 2 days ago
Joined:
7 years, 4 months ago
Email:
r*******@gmail.com

Scientist

Posts by Raygozak

<prev • 123 results • page 1 of 13 • next >
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Comment: C: GWAS principal components
... That's a good question, I'm taking over the project and I'm relatively new to GWAs, but thanks for the tip I will check this. This is how it has been done before I started, but I think it is time to revisit some of these basic assumptions about the population. ...
written 10 weeks ago by Raygozak1.3k
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GWAS principal components
... Hi, I have a question regarding the three genetic components that are used for GWAS as covariates. Given that I'm interested in a particular population, I compute the pcs from independent SNPs in my dataset and then remove outliers by visual inspection. My question is whether I should use the princi ...
gwas principal-components written 10 weeks ago by Raygozak1.3k
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Comment: C: Non -mathematical explanation of what "HMM" does (eg in GenScan)
... I would explain it as follows: as you can see in the image you attached, it's sort of like a flow diagram (https://www.sparxsystems.com.au/enterprise_architect_user_guide/14.0/guidebooks/tools_ba_data_flow_diagram.html), the difference is that it was built automatically on a set of sequences and it ...
written 5 months ago by Raygozak1.3k
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SRA data reuse policy
... If I want to re-analyze data from the SRA, how can i make sure I can do so and integrate results in publications without it being considered as misconduct? Thanks ...
data-sharing ethics sra written 5 months ago by Raygozak1.3k
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Comment: C: XMFA to MAF
... There are no C++ scripts, only C++ programs. ...
written 12 months ago by Raygozak1.3k
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Assemble small set of reads
... Hi I have a set of reads mapped to a reference sequence, what I what to do is to take the reads that map to one sequence and assemble them in a comtig as best as possible. Then I want to repeat this for thousands of sequence-read sets. I do not want to put this in a regular assember like mira, abyss ...
assembly written 3.1 years ago by Raygozak1.3k • updated 3.1 years ago by george.ry1.1k
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NCBI online blast number of hits
... Hi, Does anyone know a way to increase the number of results that can be downloaded from the NCBI interface of blast?   thanks ...
ncbi blast written 3.2 years ago by Raygozak1.3k • updated 3.2 years ago by genomax65k
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Cufflinks output verification
... Hi, does anyone know of  a way to verify that the output of cufflinks is valid, that is, that the output files have the correct structure that files of a successful run of cufflinks would have. I'm looking for a tool or something that can be implemented via scripting or programming.   Thanks ...
cufflinks written 3.2 years ago by Raygozak1.3k
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NGS alignment image drawing
... Hi, Does anyone know how can I draw programmatically a region of a bam alignment to a png image?  I want to do this to examine several bam alignments at a time.     Thanks ...
ngs bam written 3.2 years ago by Raygozak1.3k • updated 18 months ago by h.mon24k
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Cufflinks/Cuffdiff Multiple conditions
... Hi, I can see that in the CummerBund tutorial they have more than two conditions being contrasted, I'm used to doing everything pairwise even when calling cuffdif/cufflinks. How can I make many (perhaps pairwise) comparisons in a single command line call of the Cufflinks pipeline?     Thanks ...
cufflinks rna-seq written 3.2 years ago by Raygozak1.3k • updated 3.2 years ago by Sukhdeep Singh9.7k

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Popular Question 5 weeks ago, created a question with more than 1,000 views. For Cufflinks/Cuffdiff Multiple conditions
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