Question: Cufflinks for Arabidopsis.. Ensembl or TAIR 10
0
gravatar for mfahim
4.2 years ago by
mfahim10
Korea, Republic Of
mfahim10 wrote:

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.

ADD COMMENTlink modified 4.2 years ago by Antonio R. Franco4.1k • written 4.2 years ago by mfahim10
2
gravatar for Antonio R. Franco
4.2 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.1k wrote:

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 differente 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

ADD COMMENTlink written 4.2 years ago by Antonio R. Franco4.1k

Thanks Antonio..

That's a great help.. one last question.. I am interested in Alternative Splicing and novel isoforms (if any).. Any further suggestion?..

Cheers

Fahim

ADD REPLYlink written 4.2 years ago by mfahim10
1
gravatar for Antonio R. Franco
4.2 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.1k wrote:

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

ADD COMMENTlink written 4.2 years ago by Antonio R. Franco4.1k

Thanks Antonio..

I will try Limma.. I hope there is GUI.. I have little understanding of commands and programming..

 

Have a great day.

Fahim

ADD REPLYlink written 4.2 years ago by mfahim10
1
gravatar for Antonio R. Franco
4.2 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.1k wrote:

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

ADD COMMENTlink written 4.2 years ago by Antonio R. Franco4.1k
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