I need help regarding miRDeep2

Question

[kuttibiotech2009]

Hi

I am studying the miRNA expression in duck

For this

I have removed low-quality and mapped against the duck genome

Next, I would like to see known and novel miRNA using miRDeep

Before doing mirDeep2, I extracted mature and hairpin sequences of my species.

But when I extracted reference sequences, I have found less than 10 mature miRNA sequences.

So I have read some papers related to my work, where they have mentioned this "But the mapping known miRNA number was too low. As a result, two species (G. gallus, Zebra finch) were used for miRNA prediction using miRDeep2 software".

What is the meaning of this line? Please give your suggestions. it will help me a lot.

I have used the following code. I don't know whether I have given it right or not. The details of this code are given below.

miRDeep2.pl collapsed.fa Duck_genome1.fa collapsed_vs_genome.arf mature_gga_cli.fa mature_gga_cli_other.fa hairpin_gga_cli.fa -o 8

Here, in this code

I have given like mature_apl_gga_cli.fa, mature_apl_gga_cli_other.fa, hairpin_apl_gga_cli.fa

which means mature_reference sequence of Anas platyrhynchos, Columba livia, Gallus gallus, mature_other sequence of Anas platyrhynchos, Columba livia, Gallus gallus and hairpin_reference of Anas platyrhynchos, Columba livia, Gallus gallus.

Thanks in advance... Sorry for making it too long....

Sincerely KAMALAKKANNAN R
PhD scholar [e-mail]

[Ram]

A small note: While the word "doubt" is widely used in India to mean something you're unclear about, the west uses the word "question" and uses the word "doubt" to mean "suspicion". You may want to be aware of these cultural difference when interacting with an international audience.

[kuttibiotech2009]

Thank you for you comment sir...i changed it.. Please give me suggestions sir...

[Ram]

I don't know miRNA. I've helped you present your post better and add context. I'll help wherever I can help well.

Another note: There's no need to address anyone as "sir"/"madam". You can call us by our display name. I'd call you kuttibiotech2009 but you've signed off as Kamalakannan R so I can address you as either. Feel free to call me Ram.

[kuttibiotech2009]

Thanks Mr Ram.

[Ram]

Please give us a link to the paper where you read the statement you mention.