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Old 03-25-2011, 08:28 PM   #1
Tanushree
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Default miRNA Discovery

Dear All,
I am trying to make pipeline for denovo miRNA discovery so can anyone help with what can be probable methods for discovery of novel miRNA.
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Old 03-26-2011, 01:35 PM   #2
patternist
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try miRdeep, it worked for me.
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Old 03-27-2011, 08:50 PM   #3
Tanushree
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Thank you,
but can you tel me something in detail about miRdeep, i am fresher to this.
hoping for quick reply.
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Old 03-27-2011, 11:12 PM   #4
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http://www.mdc-berlin.de/en/research...eep/index.html

download the demo file, it's easy to use.
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Old 03-28-2011, 01:59 AM   #5
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Don't forget the seqanswers wiki.
For instance, looking for "mirna" gives you this.

Last edited by steven; 03-28-2011 at 02:00 AM. Reason: typo
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Old 03-28-2011, 03:07 AM   #6
Tanushree
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I am trying out miRDeep, but what should i do in the case where reference genome is not available for mapping!!
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Old 03-28-2011, 03:52 AM   #7
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mmh you can try with a related species genome.
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Old 03-28-2011, 11:11 PM   #8
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Thank U
Yes, me trying it with related species. What are the necessary filterations required before using miRDeep. Please do reply!!!!
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Old 03-28-2011, 11:44 PM   #9
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Is this suitable for Solid reads.
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Old 03-29-2011, 05:24 AM   #10
Tanushree
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I am done with the miRDeep , But how to interpret the prediction file, Especially identifying the novel miRNA
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Old 03-29-2011, 05:29 AM   #11
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You've a score for each prediction. Higher the score is, better it is.
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Old 03-29-2011, 05:38 AM   #12
Tanushree
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Is miRDeep compatible with Solid reads? How to identify novel miRNA from predicted files.
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Old 03-30-2011, 12:18 AM   #13
Bruins
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Have you read the mirDeep publication?

miRDeep
Deciphering the porcine intestinal microRNA transcriptome. (using miRDeep)
Another tool to find miRNAs in sequencing data:
MIReNA
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Old 03-31-2011, 08:36 PM   #14
Tanushree
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Thank you,
Yes i have gone through its publication. I am having the solid reads and i want to discover novel mirna for which i used mirdeep and the python script to discover them. What is the percentage of its accuracy. Can tis results be considered further.
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Old 03-31-2011, 10:55 PM   #15
NicoBxl
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miRDeep it's just a prediction tool. After that, you've to confirmed them experimentally ( custom RT-PCR stemloop per example )
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Old 05-27-2011, 01:51 AM   #16
Tanushree
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Hello!!!
How can i convert fastq files to csfasta and qual files. Is there any script for it.
Anyone please help with it.
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