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.
Please provide more information:
Do you have replicates? Does your plant have a reference genome? What is the aim of your analysis?
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
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.
the RNA sequence of the plant after and before infection they have deposited in SRA. Still am in confusion about the replicates
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.
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.
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
will go through the link and get back to you
Here are 2 papers from Nature Protocol may help you
tophat + cufflinks:
hisat + stringtie:
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.
Those require a reference genome which is not available.
read this: http://www.nature.com/nbt/journal/v29/n7/full/nbt.1883.html
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