Hello everyone,
I am using AStalavista for detecting splicing events in RNA-seq data of my Arabidopsis mutants. I found differences in...
22 results in 0.0042 seconds.
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Intron retention events with AStalavista
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Alternative splicing summary from Cuffdiff output
Hello everyone,
I want to get a kind of summarized results for all the Alternative splicing events from the Cuffdiff output,
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The difference between gene loci with isoform in RNA-seq alternative anlalysis?
As I know, 'A locus (plural loci), in genetics, is the specific location or position of a gene, DNA sequence, on a chromosome. Gene loci analysis is generally... -
Differentially expressed isoforms with Miso
Hi all,
I was recommended Miso for alternative splicing analysis. Now, I have a question on how to do this in comparison with two groups...Last edited by ninni; 01-12-2016, 01:29 AM. -
how to extract alternative splicing information from Iso-seq nonredundant sequence?
I have used pacbio SMRT Iso-seq module to analyze my cDNA sequencing data, including Getting full length reads, Isoform level clustering (ICE and Quiver),... -
Finding isoform sequences for Differentially spliced genes
I've performed RNA-Seq analysis for A. thaliana using the TopHat/Cufflinks pipeline for 2 conditions. How can I extract the sequences of all isoforms... -
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... -
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,... -
Fewer reads in the middle of some exons
Hi everyone,
I have encountered somewhat unique issue in one of my collaborators samples and would like to hear your input/thoughts.
...Last edited by rkawa; 07-01-2014, 10:25 AM. -
Quantify ration of spliced to unspliced reads
Hello,
I am interested in measuring the ratio of spliced to un-spliced genes in an RNA-seq experiment. Is there a method/technique/tool that can... -
How to get reads for a particular splice junction – TopHat and BEDTools
Does anyone have a quick way of getting all the reads that correspond to a particular splice junction? I’ve mapped my RNA-seq data with TopHat, made... -
visualize alternative splicing from cufflink output gtf file
Hi friends,
I plan to plot a figure with several alternative splicing isoforms from a locus.
I have the gtf format file... -
SplicingCompass errors: argument is of length zero
Hi,
I am testing SplicingCompass for splicing differential expression analysis. Here is the steps:
1. map the rnaseq reads to genome... -
How to detect alternative splicing when there is no replicate
I'm working on a pilot RNAseq project which compares paired-end reads between two samples, and there is only a single experiment in each sample.
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SpliceGrapher help
I have just begun using the program SpliceGrapher to visulaize alternative splicing events from my RNA seq experiment. However I am having trouble figure...
