Hi!
We have measured a protein, but we get a much larger protein than the transcript should imply.
Using RNA-seq I assembled some...
47 results in 0.0025 seconds.
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gffread to output sequence, gene_id not output
HI everyone,
Many apologies if I'm duplicating, I have searched the forums, google, can't find the specific answer.
So-... -
Warning in CuffDiff when using novel transcripts from CuffMerge as input
Hi everyone,
I am doing a differential gene expression test on RNASeq data from 64 Human Heart samples as follows:
...Code:cufflinks
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Warning in cuffmerge
The problem that I am facing is not unique one in the sense that I have seen people to face similar kind of problem from earlier posts. But unfortunately... -
Can't use my SAM files for cuffdiff
Hi everyone,
I am running a cuffdiff with GTF files from cuffmerge and SAM files from my mapped reads (CLC Bio). However, I've got error... -
A question about FPKM value in the Tophat/Cufflinks pipeline
Hi, I am a new comer of the forum. I tried to find out the answer to a question about FPKM in the pipeline Tophat/Cufflinks but I failed. So I post the... -
Cuffmerge output with missing strand information, htseq-count error
Hi everyone,
I used cuffmerge to obtain a merged.gtf file but there are 3700 entries in my merged.gtf file that contain '.' in the strand...Last edited by komalsrathi; 11-27-2013, 12:21 PM. -
cuffmerge assembly vs denovo assembly of RNAseq data
Hi all,
I have RNAseq data of stress-control of various tissue of a plant. I am doing differential gene expression. In addition, cuffmerge... -
CuffDiff cannot opn BAM file made in TopHat
I am running a number of Tuxedo pipelines, starting with TopHat and ending in CuffDiff. Most of these pipelines work fine. However, I encountered the... -
cuffDiff "cannot open reference GTF file"
I am running a series of Tuxedo pipelines and have run into the following error message a number of times in CuffDiff "cannot open reference GTF... -
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. ... -
Cuffmerge: No fasta index found for genome.fa...
Hello all,
Before running through the TopHat Cufflinks workflow with my own data, I am trying it with Drosophila_melanogaster RNA Seq data... -
splicing.dff from Cuffdiff
My workflow is tophat -> cufflinks ->cuffmerge-> cuffmerge, and I hoped to know the promoter usage and splicing events information through cuffdiff.... -
Differential gene expression analysis
I'm trying to establish the best gene expression differential analysis for my purpose: 2 genotypes, 2 experimental situations, 3 biological replicates,... -
TopHat/Cufflinks without replicates
Hi everyone,
I want to share my pipeline to analyze RNAseq data without replicates because I'm not finding the expected results, and I ask...Last edited by FoRsUs; 02-05-2013, 02:42 AM.
