[outputdir]
## Name of the output file
Output_dir=output/pacbio
[input file]
## Name of the input pacbio fasta sequence file already fixed indels/mismatches
Pacbio_reads=example/full_LR.fa
##	Gene annotation
Genome_Annotion=example/P_heterocycla_v1.0.genemodel.gff
## An annotation of transcripts Assembled in GTF format
#Cuffmerge_file=input/merged.gtf 
## directory to gmap indexes
GMAP_IndexesDir=/home/pub/gyb/TAPIS/tps/db
## name of gmap index
GMAP_IndexesName=bamboo
[Graph option]
## HEX format color
ir=#00FF00
es=#8C4726
alta=#8C0000
altd=#008C8C
altp=#006300
Exon=#0000FF
Intron=#000000
UTR=#BFBFBF
CDS=#000000
cufflinksexon=#006300
5'-5'=#1E90FF
3'-3'=#A52A2A
Fully_overlap=#90EE90
NAT_F=#0000FF
NAT_R=#008000
[GMAP option]
##Number of gmap worker threads
GMAP_Process=35
## Max length for one internal intron
MaxIntron=8000
[Polya option]
## Width of peaks when searching for poly(A) sites
Width_of_peaks=5
## Minimum distance between any two poly(A) sites
MinDist=20
## Minimum number of trusted reads supporting a poly-A site
MinSupport=1
[ati option]
## Width of peaks when searching for ati sites
Width_of_peaks=5
## Minimum distance between any two ati sites
MinDist=20
## Minimum number of trusted reads supporting a ati sites
MinSupport=1
[Global option]
## use parallel version (with <np> processors)
Multile_processing=False
[Wig option]
## if we plot wig file 
Wig_plot=True
## if we standardizing the wig 
Normaltion=True
## if the seq is Strand Specificity
Strand_Specificity=True
## lib groups 
## example: if we have four libs.two groups,use like this Lib1_Lib2 Lib3_Lib4;one group,use like this Lib1_Lib2_Lib3_Lib4;
Group=Lib1_Lib2_Lib3_Lib4_Lib5_Lib6
## wig lib,example:Lib*	libname	sorted_and_indexed_bam_file	HEX_color  
#Lib1=LB example/Lateral_bud.accepted_hits.bam.sort.bam    #FF0000
#Lib2=ST example/New_shoot_tip.accepted_hits.bam.sort.bam  #006300
#Lib3=RT example/Rhizome_tip.accepted_hits.bam.sort.bam    #458b00
Lib1=NAA1	example/NAA4h_rep1.accepted_hits.bam.sort.bam	#FF0000
Lib2=NAA2	example/NAA4h_rep1.accepted_hits.bam.sort.bam	#006300
Lib3=NAA3	example/NAA4h_rep1.accepted_hits.bam.sort.bam	#006300
Lib4=GA1	example/GA4h_rep1.accepted_hits.bam.sort.bam	#006300
Lib5=GA2	example/GA4h_rep1.accepted_hits.bam.sort.bam	#006300
Lib6=GA3	example/GA4h_rep1.accepted_hits.bam.sort.bam	#006300
## read length of seq
readLength=125
## anchorLength of aligner
anchorLength=8
## seq type pair or single
DataType=pair
[DE NAT option]
## if we complute differential nat analysis
DE=False
##
p_value_set=0.01
fdr_set=0.01
fc=0.5
DElib=Lib1_Lib2_Lib3	Lib4_Lib5_Lib6
[DE AS option]
## if we complute differential as analysis
DE=False
## p_value of two differential as sites
p_value_set=0.01
## fdr of two differential as sites
fdr=0.01
## the libs we want to perform differential apa analysis
DElib=Lib1_Lib2	Lib3_Lib4
[DE APA option]
## if we complute differential apa analysis
## this time the bam file is pas-seq 
DE=False
## Minimum distance between any two poly(A) sites
Scan_length=20
##  Minimum distance between any two poly(A) sites
#two_fisher_length=50
## two poly(A) sites ration
##fillter_ration<count1/count2<1/(fillter_ration) and fillter_ration<count2/count1<1/(fillter_ration)
fillter_ration=0.1
## p_value of two differential poly(A) sites
p_value_set=0.02
## fdr of two differential poly(A) sites
fdr=0.02
## the libs we want to perform differential apa analysis
DElib=Lib1	Lib2	Lib3
