/personalized_genomes_gbio

Primary LanguagePerl

graph_peak_call.nf

This nextflow pipeline aligns ChIP-seq data to two genome graphs, calls peaks and surjects them back to the linear reference path. It takes the following parameters:

  • --design_file: a tab separated file listing the one treatment fastq and one control fastq per line

  • --ref_graph: directory holding the reference graph. Must contain a subidrectory graphs that contains all vg files for each chromosome.

  • --pop_graph: directory holding the population graph. Must contain a subidrectory graphs that contains all vg files for each chromosome.

  • --ref_name: name prefix of xg, gbwt, gcsa indexes of the reference graph

  • --pop_name: name prefix of xg, gbwt, gcsa indexes of the population graph

  • --genome_size: size in basepairs of the species' genome

  • --chromosomes: comma separated list of chromosome names

  • --fragment_length: fragment lenght of ChIP-seq library

  • --qvlaue: false discvery rate for peak callling. Ranges between 0 and 1

  • --paired: are fastqs interleaved paired-end reads? Can be true or false

  • --peak_call: perform peak calling step? Can be true of false

  • --altered: substract reference and population graph annoatations. Can be true or false

  • --outDir: output directory

  • --time: maximum walltime for job scheduler during alignment steps

  • --mem: maximum memory allocation for job scheduler during alignment steps

pop_graph.nf

This is my custom nextflow script for creating population graphs. You should use the toil-vg construct pipeline instead from the developers of vg.

makeChains.pl

Creates a liftover file between two genomes. Unfortunately, this perl code is not readily portable.

submit_jobs_MPG and scripts

Perl pipeline for calling personalized peaks in modified reference genomes. It consists of bash and perl code that is not readily portable.

License

This code is available under GPL-3.0
Details available at: https://opensource.org/licenses/GPL-3.0