Has anyone ever looked at a GFF to find all the genes that have base overlaps ?
These genes can be counted a 0 in HTSeq and Arabidopsis is a dense...
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gene overlaps in Arabidopsis GFF file
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spliceR: problems in detecting NMD sensitivity from RNA-seq data
Hello everyone,
I want to detect the NMD sensitivity from RNA-seq data of my Arabidopsis mutants. I read that spliceR can be used for this.... -
How to find Trans gene integration position in the genome?
Hello everyone,
I was wondering how can I find where my gene of interest is integrated in the Arabidopsis genome? I have the genome sequence... -
Looking for the right tool for very-distantly-related similarity search
Hello Seqanswers,
I need some help in deciding which tool (preferably web-based) is best for searching for very-distantly related homolog... -
No plastid gene coverage in RNAseq
I am new to RNAseq and before run my counts I am looking at my files on IGV to look at coverage of some specific genes as a quick QC. I am doing my work... -
edgeR vs. DESeq vs. baySeq vs. NOIseq vs. SAMseq vs. Limma vs. Cuffdiff 2 vs. EBSeq
A recent paper suggests that cuffdiff 2 is not very sensitive and an overall poor choice for detecting differential expression in RNA-seq studies. Do... -
Wed 9/25 - Integrated Genome Browser on-line training
Join us for a live, on-line tutorial on Integrated Genome Browser:
"Focus on a Feature: Working with Sequence Data."
Date:... -
GO analysis for Arabidopsis with Goseq
Hi all,
I am trying to do a GO analysis for Arabidopsis RNA-seq data with Goseq. The software needs gene length information for all the genes but...Last edited by melis; 01-19-2012, 08:29 AM. -
Postdoc in Epigenetics available
The University of Arizona School of Plant Sciences is seeking a postdoctoral research associate with expertise in molecular biology and genetics. The... -
Bioviz Integrated Genome Browser preview - BAM and better wig support
If you are using Bioviz IGB (http://www.bioviz.org/igb) for visualization, please take a moment to try out the pre-release IGB 6.3 and let us know what...
