NCLscan.config

#############################
### NCLscan Configuration ###
#############################

## The directory of NCLscan
NCLscan_dir = 


## The directory of references and indices
## The script "create_reference.py" would create the needed references and indices here.
NCLscan_ref_dir = 


## The following four reference files can be downloaded from the GENCODE website (http://www.gencodegenes.org/).

## The reference genome sequence, eg. /path/to/GRCh37.p13.genome.fa
Reference_genome = 

## The gene annotation file, eg. /path/to/gencode.v19.annotation.gtf
Gene_annotation = 

## The protein-coding transcript sequences, eg. /path/to/gencode.v19.pc_transcripts.fa
Protein_coding_transcripts = 

## The long non-coding RNA transcript sequences, eg. /path/to/gencode.v19.lncRNA_transcripts.fa
lncRNA_transcripts = 


## External tools
bedtools_bin      = 
blat_bin          = 
bwa_bin           = 
samtools_bin      = 
novoalign_bin     = 
novoindex_bin     = 


## Bin
NCLscan_bin = {NCLscan_dir}/bin

Add_read_count_bin      = {NCLscan_bin}/Add_read_count.py
AssembleExons_bin       = {NCLscan_bin}/AssembleExons
AssembleFastq_bin       = {NCLscan_bin}/AssembleFastq
AssembleJSeq_bin        = {NCLscan_bin}/AssembleJSeq.py
append_Z3_tag           = {NCLscan_bin}/append_Z3_tag.py
FastqOut_bin            = {NCLscan_bin}/FastqOut
get_gene_name_bin       = {NCLscan_bin}/get_gene_name.py
GetInfo_bin             = {NCLscan_bin}/GetInfo
GetKey_bin              = {NCLscan_bin}/GetKey
GetNameB4Dot_bin        = {NCLscan_bin}/GetNameB4Dot
InsertInList_bin        = {NCLscan_bin}/InsertInList
JSFilter_bin            = {NCLscan_bin}/JSFilter
JSParser_bin            = {NCLscan_bin}/JSParser
JunctionSite2BED_bin    = {NCLscan_bin}/JunctionSite2BED
mp_blat_bin             = {NCLscan_bin}/mp_blat.py
PslChimeraFilter_bin    = {NCLscan_bin}/PslChimeraFilter
RemoveInList_bin        = {NCLscan_bin}/RemoveInList
RetainInList_bin        = {NCLscan_bin}/RetainInList
RmBadMapping_bin        = {NCLscan_bin}/RmBadMapping
RmColinearPairInSam_bin = {NCLscan_bin}/RmColinearPairInSam
RmRedundance_bin        = {NCLscan_bin}/RmRedundance
SeqOut_bin              = {NCLscan_bin}/SeqOut



###########################
### Advanced parameters ###
###########################

## The following two parameters indicate the maximal read length (L) and fragment size of the used paired-end RNA-seq data (FASTQ files), where fragment size = 2L + insert size. 
## If L > 151, the users should change these two parameters to (L, 2L + insert size).
max_read_len      = 151
max_fragment_size = 500


## The base quality threshold. The value should be a non-negative integer.
quality_score = 20

## The collection of the supporting reads must span the NCL junction boundary by the setting size of span range on both sides of the junction site.
span_range = 50


###################
### Performance ###
###################

## Parameters for bwa mem
## The number of threads
bwa-mem-t = 1

## Parameters for mp_blat.py
## The number of processes for running blat
##
## NOTE: The memory usage of each blat process would be up to 4 GB!
##
mp_blat_process = 1