From 70df2e4b9ad4511ce613157415333520775e8c9c Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Sun, 11 Sep 2022 13:56:53 +0200 Subject: [PATCH] Stripe extra .fastq extension form bowtie call --- Adapting_new_script_for_computing_cluster.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Adapting_new_script_for_computing_cluster.sh b/Adapting_new_script_for_computing_cluster.sh index 4cc46db..3f090c3 100755 --- a/Adapting_new_script_for_computing_cluster.sh +++ b/Adapting_new_script_for_computing_cluster.sh @@ -97,7 +97,7 @@ execute() { : Mapping $id with bowtie2 - bowtie2 --very-sensitive-local --no-mixed -p $THREADS --no-discordant --phred33 -I 10 -X 2000 -x $ebwt -1 ${f1}_val_1.fq -2 ${f2}_val_2.fq \ + bowtie2 --very-sensitive-local --no-mixed -p $THREADS --no-discordant --phred33 -I 10 -X 2000 -x $ebwt -1 ${f1%%.fastq}_val_1.fq -2 ${f2%%.fastq}_val_2.fq \ -S $id.sam >> $id\.mappingStats.txt 2>&1 : Creating BAM files for $id and filtering for paired and mapped reads