User: Raygozak

gravatar for Raygozak
Raygozak1.2k
Reputation:
1,230
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Location:
State College, PA, Penn State
Website:
http://raygozalab.org/
Last seen:
2 days, 1 hour ago
Joined:
6 years, 11 months ago
Email:
r*******@gmail.com

Scientist

Posts by Raygozak

<prev • 121 results • page 1 of 13 • next >
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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 18 days ago by Raygozak1.2k
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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 18 days ago by Raygozak1.2k
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Comment: C: XMFA to MAF
... There are no C++ scripts, only C++ programs. ...
written 7 months ago by Raygozak1.2k
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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 2.7 years ago by Raygozak1.2k • updated 2.7 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 2.7 years ago by Raygozak1.2k • updated 2.7 years ago by genomax58k
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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 2.8 years ago by Raygozak1.2k
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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 2.8 years ago by Raygozak1.2k • updated 13 months ago by h.mon21k
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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 2.8 years ago by Raygozak1.2k • updated 2.8 years ago by Sukhdeep Singh9.5k
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Answer: A: Rnaseq calibration dataset
... Just for reference I happened to find another dataset from Drosophila RNASeq. This is a simulated one.   http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32038 ...
written 3.2 years ago by Raygozak1.2k
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Rnaseq calibration dataset
... HI, i know that there is the SRA for RNASeq datasets, but is there a dataset including scripts for which i could replicate the results and be certain that i'm not doing anything wrong in my rnaseq pipeline? The description in most papers is too hand wavy and you need a lucky strike to reproduce it. ...
dataset rna-seq written 3.2 years ago by Raygozak1.2k

Latest awards to Raygozak

Popular Question 7 months ago, created a question with more than 1,000 views. For Cufflinks/Cuffdiff Multiple conditions
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