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...
9 results in 0.0021 seconds.
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Quantify ration of spliced to unspliced reads
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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... -
GFF to introns,
Hello everyone,
I am trying to get intron sequences using gff3 file (from www.phytozome.net) which have coordinates for mRNA, exon, CDS and UTR's.... -
Samtools tview: mysterious KKKK within introns.
Hi all,
I'm performing RNA-seq data analysis. I'm visualizing the alignments with samtools tview program , the attached figure shows a portion... -
Identifying intron sequences in de novo assembled transcripts?
Greetings!
We're using Trinity to do de novo assembly of frog RNA-seq data. From the resulting assemblies, I'd like to be able to identify... -
Reads within introns from polyA+ samples
Hi all,
Long time reader, first time poster.
I've been processing some RNASeq data where the RNA was isolated using a Clontech's... -
GFF to fasta (intergenic regions and introns)
Hello everyone!
I wonder if anyone knows any way of, given a gff file and the corresponding genomic segment in fasta format, extract introns and... -
Automating intron discovery in EST-derived gene models
So, yes, I have a large number of gene models that are derived from EST data. That is, the coding sequence is correct but any introns will be missing.... -
Changing Tophat 5' and 3' splice-signal criteria
Hi,
I need to change Tophat's splice signals criteria for junction calling (i.e. add more signals to those that tophat considers: ["GT-AG",...
