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MiRDeep2 (version 2.0.1.2+galaxy0)

Collapsed deep sequencing reads:

Reads in fasta format. The identifier should contain a prefix, a runningnumber and a '_x' to indicate the number of reads that have this sequence.There should be no redundancy in the sequences.

Genome:

Genome contigs in fasta format. The identifiers should be unique.

Mappings:

Reads mapped against genome. Mappings should be in ARF format.

Mature miRNA sequences for this species:

miRBase miRNA sequences in fasta format. These should be the known mature sequences for the species being analyzed.

Mature miRNA sequences for related species:

miRBase miRNA sequences in fasta format. These should be the pooled knownmature sequences for 1-5 species closely related to the species being analyzed.

Precursor sequences:

miRBase miRNA precursor sequences in fasta format. These should be the known precursor sequences for the species being analyzed.

Search in species:

If not searching in a specific species all species in your files will be analyzed. (-t)

Star sequences:

From miRBase in fasta format (optional) (-s)

Minimum read stack height:

minimum read stack height that triggers analysis. Using this option disablesautomatic estimation of the optimal value and all detected precursors are analyzed. (-a)

Maximum precursors:

Maximum number of precursors to analyze when automatic excision gearing is used. If set to -1 all precursors will be analyzed. (-g).

Minimum miRNA score:

Minimum score cut-off for predicted novel miRNAs to be displayed in the overview table. (-b)

Disable randfold analysis:

(-c)

Detailed fasta output:

Output fasta files of precursors, mature and star strand for both novel and known miRNAs

What it does

MiRDeep2 is a software package for identification of novel and known miRNAs in deep sequencing data. Furthermore, it can be used for miRNA expression profiling across samples.

Input

A FASTA file with deep sequencing reads, a FASTA file of the corresponding genome, a file of mapped reads to the genome in miRDeep2 arf format, an optional fasta file with known miRNAs of the analysing species and an option fasta file of known miRNAs of related species.

Arf format: Is a proprietary file format generated and processed by miRDeep2. It contains information of reads mapped to a reference genome. Each line in such a file contains 13 columns:

read identifier
length of read sequence
start position in read sequence that is mapped
end position in read sequence that is mapped
read sequence
identifier of the genome-part to which a read is mapped to. This is either a scaffold id or a chromosome name
length of the genome sequence a read is mapped to
start position in the genome where a read is mapped to
end position in the genome where a read is mapped to
genome sequence to which a read is mapped
genome strand information. Plus means the read is aligned to the sense-strand of the genome. Minus means it is aligned to the antisense-strand of the genome.
Number of mismatches in the read mapping
Edit string that indicates matches by lowercase 'm' and mismatches by uppercase 'M'