Dear forum,
I have 5 RNA-seq biological replicates and wish to examine the expression levels of specific genes/pathways of interest (high/low/not...
47 results in 0.0031 seconds.
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biological replicates cuffmerge?
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Cuffdiff reporting same locus several times &/or more than one gene per transcript
Hi all,
I am doing RNA-Seq of pig (Sus scrofa 10.2) and I got some weird results in cuffdiff output and I wonder if someone did ever find... -
Cuffmerge - merged.gtf - gffread - empty file
Hi!
I am using the cufflinks – cuffmerge workflow to assemble transcripts for in total 12 libraries. I now want to extract nucleotide... -
Reference annotation file (gtf) for the NOD/ShiltJ mouse?
Hi,
I am in desperately looking for a reference annotation file (gtf) for the NOD/ShiltJ mouse so that I may run Cuffmerge.
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Cuffmerge loses gene_id annotation
Dear forum readers,
I'm following the tophat2/cufflinks/cuffmerge/cuffdiff/cummeRbund workflow for my human RNA-seq data analysis. I'm... -
Differential expression using TopHat/Cufflinks, analysis by CumeRbund
I am trying to do differential expression analysis for 6 samples with no replicates
The protocol used by me after following several threads... -
Cuffmerge error file never signals "done"...is this normal?
Hello all,
I'm fairly new to the bioinformatics world and am trying to combine several gtf files with cuffmerge. My shell script is as... -
Cuffmerge error (GFaSeqGet): subsequence cannot be larger than
Hi all. I am doing some differential expression calculations using the Tuxedo pipeline. I've take all reference files (GTF, reference genome) from ensembl... -
Cufflinks problem
Hello,
I tried to get gene expression level bby using tophat/cufflinks pipeline. I follow the step exactly like the flowchart in this link:... -
Cuffmerge error
Hello, I am getting the following error message when using Cuffmerge:
cas-mw134-9sb9s:cufflinks-2.2.1.OSX_x86_64 bioadmin$ ./cuffmerge... -
Tophat error with Cuffmerged GTF
I'm trying to run Tophat 2.0.13 (bowtie 1.1.1) on colorspace csfasta and qual files using a GTF produced by Cuffmerge (Cufflinks 2.2.1) as a -G option.... -
Cuffmerge outputs only exon annotation data
Hi,
I am analyzing RNA-Seq data to discover new genes, exons and polymorphic sites. I recently aligned the RNA of 7 different tissue samples... -
cuffmerge combining genes from adjacent loci??
Hi,
After running CuffDiff, I see many of the significant genes in gene_exp.diff are annotated with multiple geneids. I have looked in the... -
cuffmerge samples from different strains or leave separate
Hi,
Possibly a naive question but I am new to RNA-seq analysis. I have RNA-seq (illumina hi-seq 100bp single end) samples from four different... -
Cuffmerge can't execute gtf_to_sam
Hi Everyone,
I am having some issues with cuff merge right now because it is giving me an error that it could not execute gtf_to_sam. I have...Last edited by thickrick99; 08-18-2014, 07:48 AM.
