Galaxy |

PEAKachu (version 0.2.0+galaxy0)

Experiment Libraries:

Control Libraries:

Pairwise Replicates:

Paired End:

Maximum Insert Size:

Features:

Sub-Features:

Select Mode:

These modes work differently.

Minimum cluster Expression Fraction:

Minimum fraction of a block in a cluster for further consideration.

Minimum Block Overlap:

Minimum fraction of the width of blocks for merging.

Minimum Block Expression:

Minimum fraction of expression of blocks for merging.

Normalisation Method:

Mad Multiplier:

Fold Change Threshold:

Adjusted p-value Threshold:

PEAKachu

PEAKachu is a tool for the accurate mapping of RBP binding sites based on CLIP-seq and RIP-seq data. PEAKachu uses signal and control libraries (ideally more than three each) to detect binding sites. It implements two peak calling approaches

adaptive

The adaptive approach applies a three-step procedure to detect regions that are significantly enriched over controls.

blockbuster is applied to the pooled libraries to combine similar sets of reads into blocks
blocks are decomposed into peaks by iteratively applying a block merging heuristic
peaks with significant enrichment of signal over control libraries are determined using DESeq2

windowed

The windowed approach subdivides the genome into overlapping regions. After filtering of lowly expressed regions and library normalization (either using manual size factors, TMM, or DESeq2), this approach determines significantly enriched windows using eiterh DESeq2 or repeated G-tests of goodness-of-fit.