NGS microRNA (smRNA) analysis

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8.7 years ago

Shahzad ▴ 30

Respected Senior,

I have NGS generated smRNA data of a plant from controlled and treated conditions. I want to analyze the deferentially expressed microRNAs in controlled and treated samples. Please guide me what is the stepwise process to follow to do this task and what tools to be used for every step. I will appreciate your help. Please ignore if you find any mistake. This thing is new for me.

Regards

next-generation-sequencing NGS microRNA miRNA • 2.8k views

ADD COMMENT • link updated 18 months ago by Ram 43k • written 8.7 years ago by Shahzad ▴ 30

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You could ask pubmed for help.

ADD REPLY • link updated 18 months ago by Ram 43k • written 8.7 years ago by David Langenberger 11k

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Dear David

Can you please suggest any research paper which can be followed for this work.

thank you.

ADD REPLY • link 8.7 years ago by Shahzad ▴ 30

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No, because I do not know what exactly you are working on. As far as I know, there are no universal bioinformatics pipelines available that can be always followed. I highly recommend you to read different publications/reviews (search in pubmed) and then design your own workflow that fits your experiment. Blind trust can be very dangerous. Never just follow a research paper.... only, if you have exact the same breadboard (machine, species, throughput, etc.). There are tools available that can help you with that, but since my focus is not on plants, I cannot recommend any.

ADD REPLY • link 8.7 years ago by David Langenberger 11k

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Hi Shzad,

can you give us more about your knowledge about NGS output data processing. What kind of output file are you working with?

ADD REPLY • link updated 4.5 years ago by Ram 43k • written 8.7 years ago by glihm ▴ 660

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