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Old 02-14-2014, 06:36 AM   #1
super0925
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Smile RNA-seq pipeline on Ion-Proton data

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!

Last edited by super0925; 02-14-2014 at 06:38 AM.
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Old 02-17-2014, 08:27 PM   #2
Jeremy
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you shouldn't double post (http://seqanswers.com/forums/showthread.php?t=40918)
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Old 02-18-2014, 12:50 AM   #3
vishnuamaram
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@ 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.
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Old 02-19-2014, 08:57 AM   #4
jfostel
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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.
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Old 02-19-2014, 09:33 AM   #5
super0925
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Quote:
Originally Posted by jfostel View Post
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!
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