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MiRDeep2 Quantifier (version 2.0.0)

Collapsed deep sequencing reads:

Reads in fasta format. (-r)

Precursor sequences:

miRNA precursor sequences from miRBase. (-p)

Mature miRNA sequences:

Mature miRNA sequences from miRBase. (-m)

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)

Sort reads by sample in PDF:

(-o)

Include ID-flexible mapping:

Also considers precursor-mature mappings that have different ids, eg let7c would be allowed to map to pre-let7a. (-k)

Skip file conversion:

(-n)

Skip mapping against precursor:

(-x)

Consider the whole precursor as the 'mature sequence':

(-w)

Discard all read multimapper:

(-U)

Upstream nucleotides:

Number of nucleotides upstream of the mature sequence to consider. (-e)

Downstream nucleotides:

Number of nucleotides downstream of the mature sequence to consider. (-f)

Allowed mismatches:

Number of allowed mismatches when mapping reads to precursors. (-g)

What it does

The module maps the deep sequencing reads to predefined miRNA precursors and determines by that the expression of the corresponding miRNAs. First, the predefined mature miRNA sequences are mapped to the predefined precursors. Optionally, predefined star sequences can be mapped to the precursors too. By that the mature and star sequence in the precursors are determined. Second, the deep sequencing reads are mapped to the precursors. The number of reads falling into an interval 2nt upstream and 5nt downstream of the mature/star sequence is determined.

Input

A FASTA file with precursor sequences, a FASTA file with mature miRNA sequences, a FASTA file with deep sequencing reads and optionally a FASTA file with star sequences and the 3 letter code of the species of interest.

Output

A tab separated file with miRNA identifiers and its read count, a signature file, a html file that gives an overview of all miRNAs the input data and a pdfs that contains for each miRNA a pdf file showing its signature and structure.