Hi all
I was following the instructions to analyze my RNASeq data with the DEXSeq package but I run into the following error while preparing...
68 results in 0.0039 seconds.
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dexseq_prepare script error with Ensembl human gtf
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Analysing only exons from ONE gene using RNAseq
I know that DEXseq and/or Cuffdiff etc. may be used of exon-levels analyses.
However, I am only interested in ONE gene, because a novel...Last edited by sindrle; 03-11-2017, 08:01 AM. -
Fit for gene/exon XXX threw the next warning(s): restarting interrupted p
Hi,
I am running DEXseq on R 3.3 and get the following warning:
...Code:Fit for gene/exon ***** threw the next warning(s): restarting
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DEXSeq and shrinkage diagnostic : Comparison between results in plotDispEsts( dxd )
I run DEXSeq on my data. I have 16 individuals in each conditions (2 conditions). After computing the dispersions with estimateDispersions( dxd ), I plotted... -
How can I use RefGene.gtf with DEXSeq
I try to convert the hg19_refGene.gtf file to a gff file with DEXseq_prepare_annotation.py. It doesn't work : my output file is empty. In DEXSeq's vignette... -
running DEXSeq with hisat2 created bam files
Hi,
I am trying to run DEXSeq with bame files made by the hisat2 mapper. I have created the gff file according to the manual. I have seen... -
DEXSeq parallelization error
Hi everyone!
I have been attempting to parallelize DEXseq on our SGE cluster using the biocparallel
method described in the latest... -
DEXseq input file
Hello!
I am trying to assess expression level of a particular gene and its isoforms in 2 treatment conditions using DEXseq.
I am new...Last edited by TPH; 02-21-2016, 08:25 PM. -
DEXseq : a known DE exon not found
Hi,
We focus on alternative splicing for one gene (with many exons).
We test several statistical methods (EdgeR, DESeq, DEXSeq)... -
DEXSeq error with paired-end data
Hi,
I'm trying to run rhe python script for counting the reads for a dexseq analysis.
But I keep getting a strange error I can't... -
DEXSeq analysis does not complete
Hi all,
I am having problem in diff. exon usage analysis of my dataset. I generated count data using protocol mentioned in DEXSeq's manual.... -
DEXSeqHTML() function from DEXSeq fails to generate the complete report
I followed the official instructions on DEXSeq biocondoctor package(data from pasilla package as suggested), and wants to generate the HTML report with... -
dexseq-count.py DEXSeq gives no results
Hello,
I am running into a bit of a problem with dexseq-count.py from DEXSeq.
dexseq-count.py. was installed and it runs... -
Problems with cufflinks GTF annotated files and DEXSeq
I'm trying to use a Cufflinks GTF that includes novel isoforms as an input for DEXSeq.
My RNA-Sseq libraries were stranded and my cufflinks command... -
Empty log2fold change rows in DEXSeq
Dear all,
I have been analyzing some Drosophila data through DEXSeq and have found that in the final results table, several rows have...
