Question: RNA seq data analysis
0
gravatar for itsanju87
2.4 years ago by
itsanju870
itsanju870 wrote:

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.

rna-seq next-gen • 1.0k views
ADD COMMENTlink modified 2.4 years ago by Czh3190 • written 2.4 years ago by itsanju870
1

Please provide more information:

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

ADD REPLYlink written 2.4 years ago by WouterDeCoster37k

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

ADD REPLYlink written 2.4 years ago by itsanju870

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.

ADD REPLYlink written 2.4 years ago by WouterDeCoster37k

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

ADD REPLYlink written 2.4 years ago by itsanju870

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.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by geek_y9.3k

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.

ADD REPLYlink written 2.4 years ago by itsanju870
0
gravatar for EVR
2.4 years ago by
EVR510
Earth
EVR510 wrote:

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

ADD COMMENTlink written 2.4 years ago by EVR510

will go through the link and get back to you

ADD REPLYlink written 2.4 years ago by itsanju870
0
gravatar for Czh3
2.4 years ago by
Czh3190
China
Czh3190 wrote:

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

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Czh3190

Follow Tophat+cufflinks protocol (Tuxedo suite) : : http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html otherwise if u dont have replicates with you then follow NOISeq Protocol.

ADD REPLYlink written 2.4 years ago by Bioblazer50

Those require a reference genome which is not available.

ADD REPLYlink written 2.4 years ago by WouterDeCoster37k

read this: http://www.nature.com/nbt/journal/v29/n7/full/nbt.1883.html

ADD REPLYlink written 2.4 years ago by Czh3190

read this: http://www.nature.com/nbt/journal/v29/n7/full/nbt.1883.html

ADD REPLYlink written 2.4 years ago by Czh3190
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