Commit ddea8893 authored by Aflitos, Saulo Alves's avatar Aflitos, Saulo Alves
Browse files

Running FRC now works

parent 718f4bd1
......@@ -17,7 +17,10 @@ done
DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
# Use a single file for logging, use the starttime as identifier
LOGFILE="FRC_heinz."`date +%Y%m%d_%k%M%S`.out
# EMBOSS path
export PATH=/home/assembly/bin/haars001/bin:$PATH
#FRC path
export PATH=/home/jvh/code/FRC_align/src:$PATH
# Input assembly
#allpaths /home/assembly/dev_150/assemblies/allpaths_lg_sample_heinz_raw/sl/data/run/ASSEMBLIES/test/final.assembly.fasta
#allpaths_454 /home/assembly/dev_150/assemblies/allpaths_lg_sample_heinz_raw_with454/sl/data/run/ASSEMBLIES/test/final.assembly.fasta
......@@ -27,13 +30,15 @@ LOGFILE="FRC_heinz."`date +%Y%m%d_%k%M%S`.out
ASSEMBLY=/home/assembly/dev_150/assemblies/allpaths_lg_sample_heinz_raw/sl/data/run/ASSEMBLIES/test/final.assembly.fasta
PREFIX=allpaths_lg
ASSEMBLY=/home/assembly/dev_150/assemblies/clc-default/clc_contigs.fa
PREFIX=clc
MIN_PE_INS=320
MAX_PE_INS=430
MIN_MP_INS=2435
MAX_MP_INS=3555
ESTIMATED_GENOME_SIZE=760000000
OUTPUT_HEADER=${PREFIX}.FRC.
# Map reads against assembly with BWA
# Create index
if [ ! -f ${PREFIX}.bwt ]
......@@ -103,15 +108,15 @@ fi
samtools index ${PREFIX}.PE.sorted.bam
# run FRC as per README
FRC --pe-sam ${PREFIX}.PE.sorted.ba \
FRC --pe-sam ${PREFIX}.PE.sorted.bam \
--pe-min-insert $MIN_PE_INS \
--pe-max-insert $MAX_PE_INS \
--mp-sam ${PREFIX}.MP.bam \
--mp-min-insert $MIN_MP_INS \
--mp-max-insert $MAX_MP_INS \
--genome-size $ESTIMATED_GENOME_SIZE \
--output $OUTPUT_HEADER \
--output $OUTPUT_HEADER
exit;
# TODO : Create better CE statisitcs
......
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