Hey All
I have analysed some RNA-Seq data for a mouse genome with both Cufflinks/Cuffdiff version 2.0 and 2.1 and get quite different results....
13 results in 0.0040 seconds.
-
Changes between Cufflinks/Cuffdiff version 2.0.2 and version 2.1.1
-
cufflinks multiple FPKM values for same location
Hi,
i have run cufflinks for my Bam files to look after the FPKM values and i got the output.
later i took the output transcripts.gtf...Last edited by abh; 04-08-2013, 10:48 AM. -
Cufflinks skips transcript models in regions with abundant reads
Hello, I am having a problem whereby Cufflinks sometimes doesn't generate models in regions with abundant reads (while performing de novo gene model prediction),... -
Cufflinks 2.0.2 segmentation fault
I am using 100 bp paired end Illumina Hi-seq data with about 50M reads and trying to use tophat / cufflinks for RNA-seq analysis for human data, using... -
where to copy samtools binary to some directories
I am installing cufflinks on my Mac OS X, and here is the instruction:
http://cufflinks.cbcb.umd.edu/tutorial.html
Under... -
Cuffdiff normalization issue
I think that CuffDiff (from cufflinks ) might have a normalization issue!
I'm using the Tophat/cufflinks/cuffdiff pipeline to analyze RNA-seq...Last edited by Kristoffer Knudsen; 02-11-2013, 06:10 AM. -
error in Cufflinks v2.0.2 when using Cuffmerge
When I run Cuffmerge, I receive the following error:
You are using Cufflinks v2.0.2, which is the most recent release.
Error creating output... -
Cufflinks 2 - error message
Hi,
I'm trying to install Cufflink2.0.2 in order to compare new version and "old" version (1.3.0) and to upgrade my pipeline. I type:... -
Cufflinks 2 - install error
Hi,
I'm trying to install Cufflink2.0.2 in order to compare new version and "old" version (1.3.0) and to upgrade my pipeline. I type:... -
problem installing cufflinks
there was no problem configuring Cufflinks v2.02 but when i make it i get an error like this
...Code:make all-recursive make[1]: Entering
Last edited by bharat_iyengar; 12-16-2012, 09:36 PM. -
Cannot find any mention of reference gff/gtf annotations in cuffmerge output
Hi,
I have been using tophat and cufflinks to analyse some RNA seq data, but cuffmerge is not behaving as I would expect.
... -
Cufflinks timing out - computing power required?
I am analysing human transcriptome data (Illumina) via the Tophat -> Cufflinks pipeline (v2.0.2) using iGenomes references. My dataset comprises 14... -
Variable results with cufflinks 2.0.2 using multiple threads
I've been doing some testing of the cufflinks 2.0.2 tools and have been getting variable results when using multiple threads. That is, running cufflinks...
