Hi,
So I'm implementing a pretty standard tuxedo pipeline on paired-end mouse data. I went along as follows.
Using the...
19 results in 0.0030 seconds.
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Cuffset number of genes too high
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Tuxedo pipeline: cufflinks with -G option vs cuffdiff with reference
Dear all,
I have been analysing RNAseq experiments using the default tuxedo pipeline for about a year, i.e., TopHat2 + cufflinks + cuffmerge... -
shiny_cuffdiff: On-the-fly interrogation and plotting of gene expression results
Hi all. I'd like to introduce the community to shiny_cuffdiff
http://nzgl.github.io/shiny_cuffdiff/
Put simply, this code... -
shiny_cuffdiff: On-the-fly interrogation and plotting of gene expression results
Hi all. I'd like to introduce the community to shiny_cuffdiff
http://nzgl.github.io/shiny_cuffdiff/
Put simply, this code uses...Last edited by danwiththeplan; 01-24-2016, 07:42 PM. -
Cuffdiff results with frag-bias-correct vary considerably when re-runing
Dear all,
I facing a very strange issue when running the tuxedo workflow with wheat data.
The problem is that I fail to... -
CummeRbund Cuffset missing genes/isoforms
I've just used the readCufflinks() function in CummeRbund to create a CuffSet instance from Cuffdiff output, but it seems there are genes and isoforms... -
Error running TopHat- "Warning: no input BAM records found"
I'm doing RNA-Seq analysis using TopHat and Cufflinks package on A. thaliana reads. When I run TopHat, I get the following error:
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Cuffdiff outputs no significant AS genes in RNA-seq analysis.
Hi All
I did my first RNA-seq analysis on A.thaliana dataset using Tophat, Cufflinks, Cuffmerge and Cuffdiff at Iplant's DE. As a beginner,... -
Tuxedo -Quantification of reference annotation o
Dear RNA-seq community,
I have run Tuxedo (and data looks good in cummeRbund) but I am wondering if should have done it slightly differently....Last edited by Gonza; 10-06-2014, 04:41 AM. -
Advice Needed on Tuxedo Suite
Hi Everyone,
I am working on a project with two groups (A & B) each containing 5 samples. Within each sample I have two RNA-seq FASTQ... -
Tuxedo Pipeline Issue - Multiple Gene Hits per Transcript, High FPKM
Hello all!
- I've been analyzing some RNA-seq data using the Tuxedo pipeline and have been getting some peculiar results, which are especially... -
GATK preprocessed bam files for cufflinks?
Hello all,
I'm relatively new to rnaseq analysis. I've been reading a lot and currently trying to come up with a reliable pipeline.
My question... -
cummeRbund - findSimilar isoforms?
Hello,
I've been using the Tuxedo suite to analyze my time series differential expression and so far I'm pretty taken by cummeRbund especially.... -
TopHat clarification for pair-end sequences
I am running paired-end RNASeq data through a Tuxedo pipeline. In the TopHat manual, it states that for the <reads1_1[,...,readsN_1]> input "this... -
Why does Cufflinks assign a strand to some RNA sequences but not others?
I am analyzing RNASeq data using a Tuxedo pipeline. For the most part, the RNA sequences seem to align with known genes in the correct orientations. ...
