Forum: Bioinformatics
08-30-2013, 04:06 PM
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Replies: 2
Views: 2,686
Different normalization methods with count data
Hello folks, Quick question. I have RNAseq count data sets which I would like to analyze together. Experimentall they are similair they only differ by their depths of coverage . One set has about 30...
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Forum: Bioinformatics
12-27-2012, 05:45 PM
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Replies: 1
Views: 2,473
generation of GTF file from a gbff?
Howdy folks, quick question .I recently pulled down some cyno genome data that included a fasta, asn, and gbff file. I create an index with bowtie2 from the fasta and ran it with no problems. I would...
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Forum: Bioinformatics
04-24-2012, 01:30 PM
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Replies: 14
Views: 4,337
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Forum: Bioinformatics
04-23-2012, 09:35 AM
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Replies: 14
Views: 4,337
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Forum: Bioinformatics
04-20-2012, 07:49 AM
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Replies: 14
Views: 4,337
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Forum: Bioinformatics
04-02-2012, 05:15 PM
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Replies: 6
Views: 3,844
PCA with cufflinks data
I was wondering if folks had any advice on the simplest way to generate a principal component analysis or MDS plot with Cufflinks output. I could group all my Cufflinks output into a data matrix and...
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Forum: Bioinformatics
02-14-2012, 10:35 AM
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Replies: 4
Views: 2,691
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Forum: Bioinformatics
02-13-2012, 03:43 PM
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Replies: 4
Views: 2,691
Best deployment method of NGS tools on a cluster?
Howdy everyone,
We are building a small rocks cluster (4-5 nodes to start) and I am hoping to configure it to perform some denovo tools (abyss and trinity) but also to be able to run the tuxedo...
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Forum: General
10-10-2011, 01:49 PM
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Replies: 0
Views: 1,457
methods journals: NGS
Can anyone recommend any methods journals that have published NGS papers? Thanks -Rich
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Forum: Bioinformatics
05-02-2011, 06:52 AM
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Replies: 16
Views: 5,811
Cool
I am definitely interested in your scripts as well. We would definitely try them with our RNAseq data. Could you please
Send them to greener@u.washington.edu
Thanks!
-Rich
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Forum: Bioinformatics
04-29-2011, 12:52 PM
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Replies: 1
Views: 2,946
Public repositories for NGS data
Hello again, Now that the NIH's public repository for NGS data is shutting down what alternative sites are folks using to upload their NGS results?
Thanks
-Rich
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Forum: Bioinformatics
04-29-2011, 12:51 PM
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Replies: 0
Views: 1,149
Looking for advice on known non-coding annotation:
Howdy folks, I wanted to get some suggestions from people on the best, most update, most detailed sources of known non-coding annotation. If I grep out the NRs from the refseq , I can get a limited...
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Forum: RNA Sequencing
04-14-2011, 09:08 PM
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Replies: 5
Views: 6,779
Is more than two conditions possible in DESEQ?
Going through the literature , it doesn't seem that you can provide more than two conditions for the negative binomial distribution. If someone knows a way to provide more than one I'd be very...
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Forum: Bioinformatics
03-08-2011, 04:49 PM
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Replies: 11
Views: 7,722
Hi Rachelly, I seem to having the same problem....
Hi Rachelly, I seem to having the same problem. My Cuffdiff output does not contain gene names. Could you post an example of a reference file that worked and the commands you ran that worked? I tried...
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Forum: Bioinformatics
02-25-2011, 03:37 PM
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Replies: 0
Views: 2,166
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Forum: Bioinformatics
02-23-2011, 07:45 AM
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Replies: 3
Views: 3,312
Thanks Reut, It was my understanding that one's...
Thanks Reut, It was my understanding that one's individual cufflinks run generate normalized FPKMs. I have run multiple cufflinks runs across conditions, time points, and with replicates. I'm curious...
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Forum: Bioinformatics
02-22-2011, 03:47 PM
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Replies: 3
Views: 3,312
Normalization of FPKMs from Cufflinks
Hi there,
I have been using the Tuxedo suite tools , specifically I have been using bowtie, tophat,and cufflinks. Now that I have FPKM values I have a couple of questions.
1. What are the most...
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