RNA-seq pipeline on Ion-Proton data

[super0925]

Hi I am a rookie bioinformatics who will process the rna-seq from Ion-proton(Single-ended).
The pipeline for processing which I know until now is
Bowtie, Tophat, Cufflinks, and cummeRbund for RNA-seq alignment, assembly, DE analysis, and .visualization.
Any other options?
Or What is this advantage or disadvantage of this pipeline?
Thank you!

[Jeremy]

you shouldn't double post (http://seqanswers.com/forums/showthread.php?t=40918)

[vishnuamaram]

@ Jeremy :

For super0925:

The pipeline looks absolutely perfect for RNAseq analysis in general.
I am not very sure of it using for Ion-proton.

Any how, why dont you give a try of using the pipeline, you do get some idea & info. from the analysis, Right.

So,go ahead, Keep posted what happens for Ion-proton RNA data.

[jfostel]

A scientist I work with recommends STAR + Bowtie 2 for RNASeq on Proton instead of TopHat. I don't think I can post a link since it's related to my job, but if you're interested in reading her poster, google "Proton RNASeq alignment", & you should find her blog post.

[super0925]

A scientist I work with recommends STAR + Bowtie 2 for RNASeq on Proton instead of TopHat. I don't think I can post a link since it's related to my job, but if you're interested in reading her poster, google "Proton RNASeq alignment", & you should find her blog post.

I found it , it seems cool!