Dear Collegues,
Lets say I have a miseq run and have the .bam file from the squencer and I would like to know how many percent of the exons...
18 results in 0.0031 seconds.
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How to get a report like stuff of a bam file how many percent of the exons are cover
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Extracting specific gene regions from BAM file using GTF
I have pooled population data in BAM format for two populations that should have local adaptations. I have identified gene regions with signatures of... -
HTSeq and repeated exons
Does anyone know how htseq-count handles reads that map to an exon that is found in two alternative transcripts of the same gene? That exon will be repeated... -
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. -
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)... -
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... -
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. -
HTSeq exon counts to gene level
Hi,
I'm working with drosophila melanogaster RNA-Seq data and at least one of my genes of interest is overlapping an other gene so I used... -
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... -
Gene Ids & description in DEXSeq html report
Hi All
I am using DEXSeq to identify differential exon usage in my dataset that has two conditions. I was able to follow all the instructions... -
Wrong exon number information from tophat-fusion
I posted this question in "BioInformatics" as well to someone who experienced similar problem with no answers. Any solutions from the RNASequencing... -
Cufflinks to find introns, sequences look wrong?
Hello,
I'm using a TopHat, Cufflinks pipeline to find intronic sequences for a species I am interested in. I run TopHat, then run Cufflinks with... -
DE exons to DE transcripts
Hi everyone,
I aligned my reads using tophat and loaded the results in R to do the DE analysis using DESeq. I feed it an exon annotation and get... -
Is there a good protocol for annotating genes and exons?
Hi,
I am running an analysis on RNASeq data, and have already detected some (putatively) novel exons and genes. What I now need to do is... -
Using DEXSeq to compare differential exon usage from different technical replicates
Hi All:
I have a general question about testing differential exon usage using DEXSeq. Suppose I have a sample called SLR (from a cell line),...
