Hi there,
I am about to run cufflinks on my TOPHAT bam files for Arabidopsis. I guess I will have to use mapped.bam files for my samples.
What reference genome should I use for cufflinks?
ENSEMBL19
or
TAIR10
I want to make sure that I get gene names instead of XLOC id in cummeRbund..
Your advice is very precious for me. Thank you.
1 answer
There is a paper around "A comprehensive evaluation of ensembl, RefSeq and UCSC annotations in the context of RNA-seq read mapping and gene quantification. Zhao and Zhang BMC Genomics (2015) 16:97 that evaluates the effect of different annotations in your data
This affects to only a small set of genes, those that are annotated in a different way in different assemblies
If this is something concerning you, use both reference genomes, and compare
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written
by
Antonio R. Franco
If using RNA-Seq, I would suggest you to use the latest version of limma under R
The vignette this program provides is very clear and intuitive
•
written
by
Antonio R. Franco
I don't think there is a GUI for limma. But you can follow the vignette (help)
There is a nice GUI for working with R and several programs for RNA-Seq analysis, but this does not include limma.
You can find it here, RNASeqGUI.
•
written
by
Antonio R. Franco
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