# This is a configuration file for fastq_screen used for assessing MII H3K36me3 and 2-cell H3K9me3 ChIP-seq data

###########
## Bowtie #
###########
## If the bowtie binary is not in your PATH then you can 
## set this value to tell the program where to find it.
## Uncomment the line below and set the appropriate location
##

BOWTIE	/usr/local/bin/bowtie
BOWTIE2	/usr/local/bin/bowtie2

############
## Threads #
############
## Bowtie can be made to run across multiple CPU cores to
## speed up your searches. Set this value to the number
## of cores you want to use for your searches.

THREADS		5

##############
## Databases #
##############
## This section allows you to configure multiple databases
## to search against in your screen. For each database
## you need to provide a database name (which can't contain
## spaces) and the location of the bowtie indices which
## you created for that database.
##
## The entries shown below are only suggested examples, you
## can add as many DATABASE sections as required, and you
## can comment out or remove as many of the existing entries
## as desired.
##
## Either the original bowtie or bowtie2 may be used for the
## mapping. Specify the aligner to use with the command line
## flag --aligner with arguments 'bowtie' or
## 'bowtie2' (default).
##
## The configuration file may list paths to both bowtie and
## bowtie2 indices. FastQ Screen automatically detects whether
## a specified index is compatible with bowtie or bowtie2.
##
## Although the configuration file may list paths to both
## bowtie and bowtie2 indices, only one aligner will be used
## for the mapping, as specified by the --aligner flag.
##
## The path to the index files SHOULD INCLUDE THE BASENAME of
## the index, e.g:
## /data/public/Genomes/Human_Bowtie/GRCh37/Homo_sapiens.GRCh37
## Thus, the indices (Homo_sapiens.GRCh37.1.bt2, Homo_sapiens.GRCh37.2.bt2, etc.)
## are found in a folder named 'GRCh37'.
##
## If the bowtie AND bowtie2 indices of a given genome reside in the SAME FOLDER,
## a SINLGE path may be provided to BOTH sets of indices.


#########
## Human - sequences available from
## ftp://ftp.ensembl.org/pub/current/fasta/homo_sapiens/dna/

DATABASE	hg19	/k/genomes/hg19/index/bowtie_canonical/hg19
DATABASE	hg19	/k/genomes/hg19/index/bowtie2_canonical/hg19

# Human rRNA index
# See /k/genomes/hg19/index/bowtie2_rrna_index/readme.txt for details of the rrna index
DATABASE        hg19rRNA    /k/genomes/hg19/index/bowtie_rrna_index/hg19_rrna
DATABASE        hg19rRNA    /k/genomes/hg19/index/bowtie2_rrna_index/hg19_rrna

#########
## Rhesus monkey 
## 

DATABASE	rheMac8	/k/genomes/rheMac8/index/bowtie_canonical/rheMac8
DATABASE	rheMac8	/k/genomes/rheMac8/index/bowtie2_canonical/rheMac8

#########
## Mouse 
## 

DATABASE	mm10	/k/genomes/mm10/index/bowtie_canonical/mm10
DATABASE	mm10	/k/genomes/mm10/index/bowtie2_canonical/mm10

#########
## Rat 
## 

DATABASE	rn6	/k/genomes/rn6/index/bowtie_canonical/rn6
DATABASE	rn6	/k/genomes/rn6/index/bowtie2_canonical/rn6

#########
## Rabbit
## 

DATABASE	oryCun2	/k/genomes/oryCun2/index/bowtie_canonical/oryCun2
DATABASE	oryCun2	/k/genomes/oryCun2/index/bowtie2_canonical/oryCun2

#########
## Guinea pig
## 

DATABASE	cavPor3	/k/genomes/cavPor3/index/bowtie_canonical/cavPor3
DATABASE	cavPor3	/k/genomes/cavPor3/index/bowtie2_canonical/cavPor3

#########
## Pig 
## 

DATABASE	susScr11	/k/genomes/susScr11/index/bowtie_canonical/susScr11
DATABASE	susScr11	/k/genomes/susScr11/index/bowtie2_canonical/susScr11

#########
## Cow
##

DATABASE	bosTau8	/k/genomes/bosTau8/index/bowtie_canonical/bosTau8
DATABASE	bosTau8	/k/genomes/bosTau8/index/bowtie2_canonical/bosTau8

#########
## Horse
##

DATABASE	equCab2	/k/genomes/equCab2/index/bowtie_canonical/equCab2
DATABASE	equCab2	/k/genomes/equCab2/index/bowtie2_canonical/equCab2

#########
## Dog
## 

DATABASE	canFam3	/k/genomes/canFam3/index/bowtie_canonical/canFam3
DATABASE	canFam3	/k/genomes/canFam3/index/bowtie2_canonical/canFam3

#########
## Sheep 
## 

DATABASE	oviAri3	/k/genomes/oviAri3/index/bowtie_canonical/oviAri3
DATABASE	oviAri3	/k/genomes/oviAri3/index/bowtie2_canonical/oviAri3

#########
## Cat
## 

DATABASE	felCat8	/k/genomes/felCat8/index/bowtie_canonical/felCat8
DATABASE	felCat8	/k/genomes/felCat8/index/bowtie2_canonical/felCat8

#########
## Chicken
## 

DATABASE	galGal4	/k/genomes/galGal4/index/bowtie_canonical/galGal4
DATABASE	galGal4	/k/genomes/galGal4/index/bowtie2_canonical/galGal4

#########
## Zebrafish
## 

DATABASE	danRer11	/k/genomes/danRer11/index/bowtie_canonical/danRer11
DATABASE	danRer11	/k/genomes/danRer11/index/bowtie2_canonical/danRer11

#########
## Drosophila melanogaster - sequence available from
## ftp://

DATABASE	dm3	/k/genomes/dm3/index/bowtie/dm3
DATABASE	dm3	/k/genomes/dm3/index/bowtie2/dm3

#########
## C.elegans

DATABASE	ce10	/k/genomes/ce10/index/bowtie/ce10
DATABASE	ce10	/k/genomes/ce10/index/bowtie2/ce10

#########
## Ecoli
## Sequence available from NCBI accession U00096
##bowtie-build /k/genomes/ecoli/fa/ecoli_sequence.fa ecoli &> bowtie-build-univec.log

DATABASE	Ecoli	/k/genomes/ecoli/index/bowtie/ecoli
DATABASE	Ecoli	/k/genomes/ecoli/index/bowtie2/ecoli

#########
## Yeast - sequence available from
## wget ftp://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/bigZips/chromFa.tar.gz
## bowtie-build `ls /k/genomes/saccer3/fa/*.fa | perl -pe "s/\n/,/g"` saccer3 &> bowtie-build-univec.log

DATABASE	Yeast	/k/genomes/sacCer3/index/bowtie/saccer3
DATABASE	Yeast	/k/genomes/sacCer3/index/bowtie2/saccer3

########
## PhiX - sequence available from Refseq accession NC_001422.1, JQ764988.2, JQ764990.1, JQ764987.1, JQ764989.1,JQ764986.1
## bowtie-build /k/genomes/phix/fa/phix_sequence.fa phix &> bowtie-build-phix.log

DATABASE	PhiX	/k/genomes/phix/index/bowtie/phix
DATABASE	PhiX	/k/genomes/phix/index/bowtie2/phix

############
## Adapters - sequence derived from the FastQC contaminats file (contaminant_list.txt from version 0.10.1) - www.bioinformatics.bbsrc.ac.uk/projects/fastqc/
## cat contaminant_list.txt | grep -v "^#" | perl -ne '/^\w+.+$/ && print' | perl -pe "s/\t+/\t/" | perl -pe "s/\r//" | awk 'BEGIN{ FS="\t"}{ print ">"$1"\n"$2 }' > contaminant_list.fa
## bowtie-build /k/genomes/adapters/fa/contaminant_list.fa adapters &> bowtie-build-phix.log

DATABASE	Adapters	/k/genomes/adapters/index/bowtie/adapters
DATABASE	Adapters	/k/genomes/adapters/index/bowtie2/adapters

##########
## Vector - Sequence taken from the UniVec database
## wget ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec_Core
##bowtie-build /k/genomes/univec/fa/UniVec_Core.fa univec &> bowtie-build-univec.log

DATABASE	Vectors		/k/genomes/univec/index/bowtie/univec
DATABASE	Vectors		/k/genomes/univec/index/bowtie2/univec

##########
## Wasp - In house custom database

#DATABASE	Wasp		/data/public/Genomes/Wasp_transcriptome/wasp_transcriptome	
