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RNA seq data analysis

hi everyone, I am new to NGS analysis field. I have RNA seq data of a plant after infection and healthy plant data at three stages. What insilico analysis can be done with this data and what softwares can be used. Can anyone guide me with this.

next-gen rna-seq
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updated by Czh3 Czh3 • written by itsanju87 • itsanju87

Please provide more information:

Do you have replicates? Does your plant have a reference genome? What is the aim of your analysis?

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written by WouterDeCoster WouterDeCoster

genome of the organism is not yet completed. I have to do some transcriptome data analysis using the RNA seq data. I don understand what is replicates

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written by itsanju87 • itsanju87

Replicates: preparing RNA-seq libraries for multiple samples (technical or biological) for the same condition.

In contrary to what is commonly thought, an RNA-seq experiment isn't completely hypothesis free. You cannot just sequence something and "let the data tell you what's going on". You need a biological hypothesis.

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written by WouterDeCoster WouterDeCoster

the RNA sequence of the plant after and before infection they have deposited in SRA. Still am in confusion about the replicates

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written by itsanju87 • itsanju87

Do you have a supervisor or a colleague to ask about ? It will be good to discuss with someone if you have to start both biology and informatics from scratch. Definitely people here helps you, but thats a long way if you need to do something, without knowing basics and without having specific goal in mind.

I don't mean to discourage in anyway, but online forums helps you keep going if you are stuck with something but its not going to be a "complete" guidance.

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written by GouthamAtla GouthamAtla

my supervisor don't have exposure in this field. My colleagues also working on different area. Anyway i know few working on this so that i can get assistance from them.

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written by itsanju87 • itsanju87

Hello Dear

We are going to held 3 days NGS data Analysis training at our Genome Education Centre, Bangalore. The workshop is specifically designed for Biologists interested in learning about Next Generation Sequencing (NGS) Technology and specifically, Informatics challenges and Bioinformatics methodology and pipelines used for analysis of data generated using NGS technology.

The workshop will include extensive hands-on practical sessions and focused classroom presentations to introduce the participants to the Genome Informatics tools available for analysis of Next Generation Sequencing

For more details please write to me directly: piyush@bionivid.com

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written by piyushkumartiwari • piyushkumartiwari

2 answers

hi,

If you are new to NGS data analysis take a look "https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification" . Its quite easy and well documented. If you are not comftable with programming, then you can try Chipster, a online tool for NGS data analysis

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written by EVR EVR

will go through the link and get back to you

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written by itsanju87 • itsanju87

Here are 2 papers from Nature Protocol may help you

tophat + cufflinks: http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html

hisat + stringtie: http://www.nature.com/nprot/journal/v11/n9/full/nprot.2016.095.html

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written by Czh3 Czh3

Those require a reference genome which is not available.

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written by WouterDeCoster WouterDeCoster

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