From 46b674062301c3cb816b294dbb97347dc3885cb4 Mon Sep 17 00:00:00 2001 From: yzheng74 Date: Fri, 27 Apr 2018 21:04:44 -0500 Subject: [PATCH] rename cutsite --- s1_bwaAlignment.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/s1_bwaAlignment.sh b/s1_bwaAlignment.sh index bf08d28..fcc01f4 100644 --- a/s1_bwaAlignment.sh +++ b/s1_bwaAlignment.sh @@ -46,7 +46,7 @@ do # step1.3 - trim and filter unmapped echo "Step1.3 - Trim unmapped reads until the restriction enzyme cutting site." $samtoolsDir/samtools fastq $resultsDir/$name\_unmapped_$i.sam >$resultsDir/$name\_unmapped_$i.fastq - $bin/cutsite_trimming_Ye --fastq $resultsDir/$name\_unmapped_$i.fastq --cutsite $cutsite --out $resultsDir/$name\_unmapped_trim_$i.fastq --rmuntrim + $bin/cutsite_trimming_mHiC --fastq $resultsDir/$name\_unmapped_$i.fastq --cutsite $cutsite --out $resultsDir/$name\_unmapped_trim_$i.fastq --rmuntrim awk -v minLen=$seqLength 'BEGIN {OFS = "\n"} {header = $0 ; getline seq ; getline qheader ; getline qseq ; if (length(seq) >= minLen) {print header, seq, qheader, qseq}}' < $resultsDir/$name\_unmapped_trim_$i.fastq >$resultsDir/$name\_unmapped_trim_filter_$i.fastq