Skip to content

loosolab/master_project_JLU2018

6d5c604c29
Switch branches/tags

Name already in use

A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?
Go to file
Code

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
fix
December 14, 2018 08:05
December 15, 2018 23:10
December 12, 2018 17:56
fix
December 14, 2018 08:05

masterJLU2018

De novo motif discovery and evaluation based on footprints identified by TOBIAS

For further information read the documentation

Dependencies

Installation

Start with installing all dependencies listed above. It is required to set the enviroment paths for meme-suite. this can be done with following commands:

export PATH=[meme-suite instalation path]/libexec/meme-[meme-suite version]:$PATH
export PATH=[meme-suite instalation path]/bin:$PATH

Download all files from the GitHub repository. The Nextflow-script needs a conda enviroment to run. Nextflow can create the needed enviroment from the given yaml-file. On some systems Nextflow exits the run with following error:

Caused by:
  Failed to create Conda environment
  command: conda env create --prefix  --file env.yml
  status : 143
  message:

If this error occurs you have to create the enviroment before starting the pipeline. To create this enviroment you need the yml-file from the repository. Run the following commands to create the enviroment:

path=[Path to given masterenv.yml file]
conda env create --name masterenv -f=$path

When the enviroment is created, set the variable 'path_env' in the configuration file as the path to it.

Important Note: For conda the channel bioconda needs to be set as highest priority! This is required due to two differnt packages with the same name in different channels. For the pipeline the package jellyfish from the channel bioconda is needed and NOT the jellyfisch package from the channel conda-forge!

Quick Start

nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta [FASTA-file] --motif_db [MEME-file] --config [UROPA-config-file]

Parameters

For a detailed overview for all parameters follow this link.

Required arguments:
	--bigwig		 Path to BigWig-file
	--bed			 Path to BED-file
	--genome_fasta		 Path to genome in FASTA-format
	--motif_db		 Path to motif-database in MEME-format
	--config		 Path to UROPA configuration file
	--create_known_tfbs_path Path to directory where output from tfbsscan (known motifs) are stored.
				 Path can be set as tfbs_path in next run. (Default: './')
	--out			 Output Directory (Default: './out/')	
	
Optional arguments:
	
	--help [0|1]		1 to show this help message. (Default: 0)
	--tfbs_path 		Path to directory with output from tfbsscan. If given tfbsscan will not be run.

	Footprint extraction:
	--window_length INT	This parameter sets the length of a sliding window. (Default: 200)
	--step INT		This parameter sets the number of positions to slide the window forward. (Default: 100)
	--percentage INT	Threshold in percent (Default: 0)

	Filter unknown motifs:
	--min_size_fp INT	Minimum sequence length threshold. Smaller sequences are discarded. (Default: 10)
	--max_size_fp INT	Maximum sequence length threshold. Discards all sequences longer than this value. (Default: 100)

	Clustering:
	Sequence preparation/ reduction:
	--kmer INT		Kmer length (Default: 10)
	--aprox_motif_len INT	Motif length (Default: 10)
	--motif_occurence FLOAT	Percentage of motifs over all sequences. Use 1 (Default) to assume every sequence contains a motif.
	--min_seq_length Interations	Remove all sequences below this value. (Default: 10)

	Clustering:
	--global INT		Global (=1) or local (=0) alignment. (Default: 0)
	--identity FLOAT	Identity threshold. (Default: 0.8)
	--sequence_coverage INT	Minimum aligned nucleotides on both sequences. (Default: 8)
	--memory INT		Memory limit in MB. 0 for unlimited. (Default: 800)
	--throw_away_seq INT	Remove all sequences equal or below this length before clustering. (Default: 9)
	--strand INT		Align +/+ & +/- (= 1). Or align only +/+ (= 0). (Default: 0)

	Motif estimation:
	--min_seq INT 		Sets the minimum number of sequences required for the FASTA-files given to GLAM2. (Default: 100)
	--motif_min_key INT	Minimum number of key positions (aligned columns) in the alignment done by GLAM2. (Default: 8)
	--motif_max_key INT	Maximum number of key positions (aligned columns) in the alignment done by GLAM2.f (Default: 20)
	--iteration INT		Number of iterations done by glam2. More Iterations: better results, higher runtime. (Default: 10000)
	--tomtom_treshold float	Threshold for similarity score. (Default: 0.01)
	--best_motif INT	Get the best X motifs per cluster. (Default: 3)

	Moitf clustering:
	--cluster_motif	Boolean	If 1 pipeline clusters motifs. If its 0 it does not. (Defaul: 0)
	--edge_weight INT	Minimum weight of edges in motif-cluster-graph (Default: 5)
	--motif_similarity_thresh FLOAT	Threshold for motif similarity score (Default: 0.00001)

	Creating GTF:
	--organism [hg38 | hg19 | mm9 | mm10]	Input organism
	--tissues List/String 	List of one or more keywords for tissue-/category-activity, categories must be specified as in JSON
				config
All arguments can be set in the configuration files

For further information read the documentation