MiRDeep2 identification of novel and known miRNAs

I think i just need to return the processor mirna format to the original format after converting RNA/DNA(original format cant be used for RNA/DNA convector). I think the reference and mature and my data are fine. Do understand what im saying ?
question is how change the processor mirna to the original format/ I think you misunderstanding me in last post . Off course my mistake , my English need more practice:sweat_smile:

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Do you mean that you want to wrap this fasta sequence again?

Either the NormalizeFasta or FASTA Width formatter tool can be used. 80 bases is the most common (and original) wrapped length for fasta data.

Also – all bases need to be ATCGN. If you have IUPAC characters in your data, change those to “N”. The tool manual links I shared before have example data. Lines that have any characters other than ATCGNU are rejected. And Ts in some of your inputs and Us in others will create conflicts (last error you reported).

You see this error
fasta_nucleotide_changer: Invalid input: This looks like a multi-line FASTA file.
Line 3 contains a nucleotides string instead of a ‘>’ prefix.
FASTX-Toolkit can’t handle multi-line FASTA files.
Please use the FASTA-Formatter tool to convert this file into a single-line FASTA.

cat: write error: Broken pipe

So if i change this format the Mirdeep2 doesnt recognize this data as processor mirna. So i have to change it with some tool like FASTA Width formatter and then convert it to DNA and after than return it to original format as it be at the first time . Do you think this idea is wrong ?

@amir were you able to resolve the mirdeep2 issues you encountered?

No. At last i chose different path. Some thing is wrong about it. and i didnt figure it out

@amir That’s unfortunate. would you mind sharing your new strategy for analysis? I got up to mapping and quantification, but the novel RNA analysis never worked.

I am using Bowtie for mapping. bowtie1 not 2. You should first map you data to rRNA. and then Map the “UnMaps” to the hairpins transcripts from MirBase. Forget about the mirdeep2. I put much time on it and never got any results

I actually think I figured it out now; hopefully, I’m getting the right results. The key is normalizing all the fasta (genome, mature, and hairpin).

i did that too. anyway wish u the best