/bcfngs_Mapping_automation

workflow for the bcfngs core facility at

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Mapping automation

workflow for the bcfngs core facility at

This is an internal how to for the workflow of the automation for the bcfngs.

genome indexing

This steps needs to be run onyl once. unless new genomes are added.

this is all run on the hpcl5002.

  1. log-in to the server.
  2. If not done before, activate the conda environment inside a screen, so that one can log out from the server and still run the workflow in the background. More information about the is in the github web site.
  3. open the config.yaml file, e.g. vi /fs/pool/pool-bcfngs/scripts/config.yaml and add the genome links from the ensembl FTP site in this format:
  Dps.3.0.45:
    fasta: "ftp://ftp.ensemblgenomes.org/pub/metazoa/release-45/fasta/drosophila_pseudoobscura/dna/Drosophila_pseudoobscura.Dpse_3.0.dna.toplevel.fa.gz"
    gtf: "ftp://ftp.ensemblgenomes.org/pub/metazoa/release-45/gtf/drosophila_pseudoobscura/Drosophila_pseudoobscura.Dpse_3.0.45.gtf.gz"
  1. run the command snakemake -nps ../scripts/getGenome_IndexGenome.Snakefile to check that the new genome is added to the workflow (the -n is a dry-run which just output the command without performiong it.)
  2. run the same command without the -n - snakemake -ps ../scripts/getGenome_IndexGenome.Snakefile. This will download the fastA and gtf files from the given links and create the index files for them as well.

Mapping

Mapping woill be done with the STAR aligner for a specific genome either in a paired-end or singel-end format.

Changing parameters before mapping

The following settng must be adjusted before running the script:

######## Project Setting
# To create a separate project results folder for each run, change the name of the project here.
project: "P152"
# this path would point to the raw data in fastq format. This must be changed each time for the correct data to be analyzed.
path: "/fs/pool/pool-bcfngs/fastq_files/P146/P152_ChIP_Asx_5_6/conc.fastq"
# Which organism to map the data to
org: "Dme.BDGP6.22"

The project and the path should point to the current project which is being mapped.

the org must be the organism the data is mapped against. The term must be identical to the term in the list of organisms from the config files.

running the star mapping step.

first change the working directory to the path of the actual project on the pool-bcfngs. e.g.

cd /fs/pool/pool-bcfngs/fastq_files/P000/P000_Testrun/conc.fastq/

Next run the snakemake script first as a dry-run (-n) and if all seems well than for real.

e.g.

# for single-end samples
snakemake -nps /fs/pool/pool-bcfngs/scripts/Star.MappingQuant.SingleEndFastq.Snakefile -j 50
# for paired-end samples
snakemake -ps /fs/pool/pool-bcfngs/scripts/Star.MappingQuant.PairedEndFastq.Snakefile -j 50