example.clean.RNAseq.input

#example input file to clean RNAseq reads prior to assembly (January 2014)

#input fastq files (make sure left and right match up in the order)
#path to paired end files
files=/PATH/TO/FILES/
#files
file1=( \
SAMPLE1_1.fastq.gz \
SAMPLE2_1.fastq.gz \
)
file2=( \
SAMPLE1_2.fastq.gz \
SAMPLE2_2.fastq.gz \
)
#id
id=( SAMPLE1 SAMPLE2 )

#general parameter
minlen=30	#minimum read length to output in final file

#trimmomatic parameters
adapter=/storage/data_1/megan/programs/rnaseq_scripts/adapter.fasta
score=-phred33	#-phred33 or -phred64
headCropLen=6
seedMismatches=2
palindromeClipThreshold=30
simpleClipThreshold=12
windowSize=4
windowQuality=20
leadQuality=10
trailQuality=10
path_trimmomatic=/storage/data_1/megan/programs/Trimmomatic-Src-0.22/trimmomatic-0.22/dist/jar/trimmomatic-0.22.jar
#MIN_PREFIX=8 path_trimmomatic=/usr/local/bin/Trimmomatic-0.22/trimmomatic-0.22.jar

#flash parameters
minOverlap=15
maxOverlap=70 #or calc from readlen, frag len, sd [70 is default for 100bp reads, 180bp frag, 18sd]
maxMismatchDensity=0.2
phredOffset=33

#Quake/Jellyfish parameters
#quakeK=19
#cov_cut=1
#path_quake=/storage/data_1/megan/programs/Quake

#misc system and log files
threads=6
resourcelog=resource.log

#email for notification
email=YOU@DOMAIN.COM