settings.conf.backup

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Settings file for haploid enrichment screen scripts
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Description:
All parameters are tab separated. Don't edit the name of the parameter.



# These	settings are always required (ie. for additional_gene_mapping.sh and additional_gene_mapping.sh)
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Parameter	value   description
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gene_ref:	/scratch/ENRICHMENT/ref/HG19_ref_unique.BED		# File containing list with genes and their genomic position
ref_id:	unique		# A human readable and somewhat	comprehensive tag for this gene reference file (for example concatenated or unique)
core_num:	20		# Desired number of CPU cores to be used
memory_limit:	20G		# Amount of RAM available for analysis



# These settings are only applicable to the Full Analysis Pipeline (ie. full_enrichment_analysis.sh)
######################################################################################################
Parameter	value   description
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location_bowtie :	/usr/local/bin/bowtie	# enter full path
ref_genome:	/scratch/reference_files/BOWTIE_HG19/hg19	# path to directory incl. invariable part of file name
control_dataset:	/media/analyzed_data/enrichment_screens/control_data_HG19/seq.fastq.uniqReads_mapped_UNIQ	
trim_reads:	yes	# 'yes' or 'no'
keep_reads_from:	0	# from which base should the reads be kept? (0 for beginning of read)
desired_read_length:	50	# new read length
mismatch_num:	1	# Number of mismatches allowed, cannot be more the 1
final_dir:	/media/analyzed_data/enrichment_screens/	# To which directory should the files be written to if the analysis is done (please put / behind it!)