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multimapp generation update

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ozgunharmanci committed Mar 14, 2019
1 parent a084f4a commit 47ada2aea00be9093fde3620bddd893a10e75a86
Showing with 2 additions and 2 deletions.
  1. +2 −2 bin/generate_multimappability_signal.csh
@@ -7,7 +7,7 @@ fi

fasta_fp=$1;
l_read=$2;
bt2_prefix=$3;
abs_bt2_prefix=$3;

if [ ! -e $fasta_fp ]
then
@@ -35,7 +35,7 @@ rm -f temp_map_reads.csh
for chr_id in ${chr_ids[@]}
do
mkdir temp/${chr_id}
echo "MUSIC -fragment_sequence_2_stdout temp/${chr_id}.bin ${l_read} read | bowtie2 -x ${bt2_prefix} -k 5 -p 4 -f -S /dev/stdout -U - | MUSIC -preprocess SAM stdin temp/${chr_id}" >> temp_map_reads.csh
echo "MUSIC -fragment_sequence_2_stdout ${PWD}/temp/${chr_id}.bin ${l_read} read | bowtie2 -x ${abs_bt2_prefix} -k 5 -p 4 -f -S /dev/stdout -U - | MUSIC -preprocess SAM stdin ${PWD}/temp/${chr_id}" >> temp_map_reads.csh
done
chmod 755 temp_map_reads.csh

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