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moca_blue

[2023-06-07]

MOCA BLUE

MOtif Characterization & Annotation from DEEP LEARNING feature enrichment

Welcome the the moca_blue suite! from Simon M. Zumkeller RStudio 2022.07.2 Build 576

This is a tool-box for the analyses of DNA motifs that have been derived from deep-learning model features extraction. moca_blue is currently in development.

Please find more detailed descriptions of the directories and their role within them, respectively.

This is a pipeline of consecutive operations that can be and will be availabe here.

INPUT DIRECTORY /0MOTIFS /ref_seq - HDF5.file [feature extraction files] - fastas |____________ - gffs | | - meta-data START DIRECTORY /mo_nom /mo_range | output - get motif patterns - get motif meta-data | - motif annotation | | - motif modification | |_____________________________________| | | /mo_clu MAPPING to reference (external) - analyze motifs | use e.g. "blamm - compare/cluster | (https://github.com/biointec/blamm) | cp occurences.txt [results] /mo_proj || | /mo_proj - filter for meaningful matches - interpret model predictions - gene annotation - module generation

mo_nom --------------------------

Extract motifs from MoDisco hdf5 files and assign nomenclature. Currently, there are three versions of the same script that can be used for the extraction of a given format of weight matrix.

rdf5_get_xxx_per_pattern.v1.0R.R

PFM - positional frequence matrix PWM - positional weight matrix (best for clustering/comparison) CWM - contribution weight matrix (best for mapping)

mo_range ------------------------

Motifs/ EPMs are not distributed at random in a genome. To optimize the search for motifs/EPMs in a genome or gene-space, these tools extract the positionally preferred ranges for each motif/EPM in a hdf5 file.

rdf5_get_seql_per_patternV2.R - Extract a list of seqlets and their positions from the hdf5 file

meta_motif_ranges_characteristics_TSS-TTS.1.1.R - Producee a table from the rdf5_get_seql_per_patternV2.R output that provides the gene-space statistics for each motif/seqlet in reference to transcription start and stop sites (TSS, TTS)

mo_clu --------------------------

Analyse and Edit motif-files stored in jaspar-format here. Results should be stored in the "out" directory.

mo_cluster_v2.0R - generates dendrograms/trees based on distancy-matrix for different models.

mo_old ---------------------------

Old and outdated scripts used for the moca_blue suite are stored here.

ref_seq -------------------------

Store genome data like fasta, gff and many more here for INPUT.

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