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Small RNA Signatures (version 3.5.0)

Compute signature from this bowtie standard output:

Min size of query small RNAs:

'23' = 23 nucleotides

Max size of query small RNAs:

'29' = 29 nucleotides

Min size of target small RNAs:

'23' = 23 nucleotides

Max size of target small RNAs:

'29' = 29 nucleotides

Minimal relative overlap analyzed:

'1' = 1 nucleotide overlap

Maximal relative overlap analyzed:

'1' = 1 nucleotide overlap

Graph type:

Signature can be computed globally or by item present in the alignment file

Maximum of Y-scale of the Numbers-of-pairs plot:

Interger. Leave 0 for self-determination of Y-scale

Maximum of Y-scale of the Number-of-pairs-Z−scores plot:

Integer. Leave 0 for self-determination of Y-scale

Maximum of Y-scale of the Overlap-probabilities plot:

Percent value as an Integer. Leave 0 for self-determination of % Y-scale

Maximum of Y-scale of the Overlap-probabilities-Z−scores plot:

Interger. Leave 0 for self-determination of Y-scale

What it does

Compute small RNA (piRNA, siRNA, ...) signatures.

This tool computes (i) the number of pairs aligned reads by overlap classes (in nt) and associated z-scores, and (ii) the ping-pong signal (Brennecke et al. Science. 2008;322: 1387–1392) and associated z-scores.

Note that the number of pairs of aligned reads is disctint from the number of pairs of reads when these reads can be aligned at multiple positions in the genome. The two values are equal only when the analysis is restricted to uniquely mapping reads.

Options set the min and max size of both the query small rna class and the target small rna class, the range of overlaps (in nt) over which to compute the signatures, and whether the signatures should be reported at genome-wide level or by item (chromosomes, genes, etc.). For details on computational algorithmes for piRNA and siRNA signatures, see Antoniewski (2014).

Input

A sorted BAM alignment file.

Outputs

Global: The number of pairs found, the ping-pong signal and the associated z-scores are computed at genome-wide level and returned in a pdf file.

Lattice: The number of pairs found, the ping-pong signals and the associated z-scores are computed for each items described in the BAM alignment input and returned in a pdf file as a lattice graph.