User: Raygozak

gravatar for Raygozak
Raygozak1.1k
Reputation:
1,140
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Location:
State College, PA, Penn State
Website:
http://raygozalab.org/
Last seen:
1 year, 2 months ago
Joined:
5 years, 11 months ago
Email:
r*******@gmail.com

Scientist

Posts by Raygozak

<prev • 118 results • page 1 of 12 • next >
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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 21 months ago by Raygozak1.1k • updated 21 months ago by george.ry1.0k
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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 21 months ago by Raygozak1.1k • updated 21 months ago by genomax37k
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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 21 months ago by Raygozak1.1k
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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 21 months ago by Raygozak1.1k • updated 6 weeks ago by h.mon9.2k
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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 22 months ago by Raygozak1.1k • updated 22 months ago by Sukhdeep Singh9.0k
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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 2.2 years ago by Raygozak1.1k
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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 2.2 years ago by Raygozak1.1k
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Comment: C: how to extract AIC(Akaike's Inforation Criterion) in LAR(Least Angle Regression)
... Have you tried asking in http://stats.stackexchange.com/? ...
written 3.2 years ago by Raygozak1.1k
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Comment: C: How To Efficiently Parse A Huge Fastq File?
... You can always concatenate files downloaded from SRA or generate one with random sequences/qualities to obtain a file of any size. ...
written 3.2 years ago by Raygozak1.1k
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Comment: C: Artificial Sequences in ncbi
... Well, I did check univec but it is in fasta format, which is useless to me. thanks though. ...
written 3.3 years ago by Raygozak1.1k

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