ebio/dekupl repository overview

⁠DE-kupl

DE-kupl is a pipeline that finds differentially expressed k-mers between RNA-Seq datasets.

Dekupl-run handles the first part of the DE-kupl pipeline from raw FASTQ to the production of contigs from differentially expressed k-mers.

• REFERENCES: DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition Jérôme Audoux, Nicolas Philippe, Rayan Chikhi, Mikaël Salson, Mélina Gallopin, Marc Gabriel, Jérémy Le Coz, Emilie Drouineau, Thérèse Commes and Daniel Gautheret https://doi.org/10.1186/s13059-017-1372-2⁠

• DOCKER CREATOR and MAINTAINER: Emilie Drouineau: [email protected]⁠

• For any question, please contact: eBio: [email protected]⁠

⁠Run DE-kupl

• CONFIGURATION (config.json)

• fastq_dir: Location of FASTQ files

• nb_threads: Default number of thread to use (unless specified in the snakemake command-line

• kmer_length: Length of k-mers (default: 31). This value shoud not exceed 32.

• lib_type: Paired-end library type (default: rf). You can specify either rf for reverse-forward strand-specific libraries, fr for strand-specific forward-reverse, or unstranded for unstranded libraries.

• output_dir: Location of DE-kupl results (default: DEkupl_result).

• dekupl_counter:

  • min_reccurence: Minimum number of samples to support a k-mer
  • min_recurrence_abundance: Min abundance threshold to consider a k-mer in the reccurency filter.

• Ttest:

  • condition: Specify A and B conditions.
  • pvalue_threshold: Min p-value (adjusted) to consider a k-mer as DE. Only DE k-mers are selected for assembly.
  • log2fc_threshold: Min Log2 Fold Change to consider a k-mer as DE.

• Samples: An array of samples. Each sample is described by a name and a condition. The FASTQ files for a sample will be located using the following command fastq_dir/sample_name_{1,2}.fastq.gz

• FAQ If new samples are added to the config.json, make sure to remove the sample_conditions.tsv file in order to force SnakeMake to re-make all targets that depends on this file

• OPTIONS:

-test

get data to test the pipeline

-getconf

get the default configuration file to run dekulp (config.json)

-nbthread

fix the thread numbers when running, by default value=1

-run

run dekupl with the config file

• RUN DOCKER: docker run --rm --privileged -v $(pwd):/data ebio/dekupl -nbthread NB -run

⁠GIT REPOSITORY

• Git official repository: GitHub Pages⁠

⁠Tool versions

• R v3.3.2
• Python v3.4.3
• Snakemake v3.10.1
• GSNAP: 2017-01-14
• perl v5.18.2