#
## this is a configuration file for processingUnique.sam script
#
## it will contain all the necessary informations for
# 
## AS event file name
## data type (single-end or paired-end)
## base of the experiment
## list of sam files
## etc..
## 
#

####################################
### readLength
### 
-readLength = 72
#

####################################
### junctionLength: it can be calculated as 
###   junctionLength = 2*(readLength-anchorLength)
#
### For example, if your readLength is 50 and you ran tophat with -a/--min-anchor-length 8
### junction length becomes 2*(50-8) = 84
#
-junctionLength = 142
#

#####################################
### AS file name
### AS event file names
### it currently support 5 AS event types
### full path here
#
-SE = /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9-frstrand/ASEvents/fromGTF.SE.txt
-MXE = /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9-frstrand/ASEvents/fromGTF.MXE.txt
-A5SS = /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9-frstrand/ASEvents/fromGTF.A5SS.txt
-A3SS = /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9-frstrand/ASEvents/fromGTF.A3SS.txt
-RI = /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9-frstrand/ASEvents/fromGTF.RI.txt
#

####################################
### experiment name
-experiment = RNASeq
#


####################################
### base name for sample_1 and sample_2
-base_1 = SAMPLE_1
-base_2 = SAMPLE_2
#


######################################
### data type
### single-end or paired-end
#
#-dataType = single
#-dataType = paired
-dataType = paired
#


######################################
### library type
### fr_unstranded, fr_firststrand, fr_secondstrand
#
#-libType = fr-unstranded
#-libType = fr-firststrand
#-libType = fr-secondstrand
-libType = fr-firststrand


######################################
### sam file folder
### user can put all sam files in the same place (probably using "symbolic link") 
#
-samDir = 

######################################
### out file folder
### MATS input file will be in this folder
#
-outDir = /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9-frstrand/temp


#
#####################################
### sam file name
###
#-input_1 = unique.ESRP.1.sam
-input_1 = /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9-frstrand/SAMPLE_1/REP_1/aligned.sorted.bam,/dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9-frstrand/SAMPLE_1/REP_2/aligned.sorted.bam,/dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9-frstrand/SAMPLE_1/REP_3/aligned.sorted.bam,/dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9-frstrand/SAMPLE_1/REP_4/aligned.sorted.bam
#-input_2 = unique.EV.1.sam
-input_2 = /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9-frstrand/SAMPLE_2/REP_1/aligned.sorted.bam,/dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9-frstrand/SAMPLE_2/REP_2/aligned.sorted.bam,/dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9-frstrand/SAMPLE_2/REP_3/aligned.sorted.bam,/dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9-frstrand/SAMPLE_2/REP_4/aligned.sorted.bam


###################################
### alert email
### email address to receive pipleline progress (error, warning, or end of process)
### change this to your email address
-email = yourmail@domain.com
#
#