Differences

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--- scripts:alignment [2025/03/08 15:41] – Align your reads to a reference genome 37.26.174.181
+++ scripts:alignment [2025/04/09 12:05] (current) – [Daughter script] 37.26.174.181
@@ Line 67: / Line 67: @@
 for fastq_1 in "$input_dir"/*_1.{fastq,fq}.gz; do
     if [[ -f "$fastq_1" ]]; then
-        fastq_2="${fastq_1/_1/_2}"
+        fastq_2="${fastq_1/_1․/_2․}"
         if [[ -f "$fastq_2" ]]; then
             align "$fastq_1" "$fastq_2" "$output_dir" "$reference" "$threads"
@@ Line 83: / Line 83: @@
 #SBATCH --mem=40gb
 #SBATCH --cpus-per-task=8
-#SBATCH --output=../log/align_00.%j.log  # %j will be replaced with the job ID
+#SBATCH --output=../log/align_00.log
 #SBATCH --job-name=align_mydata
@@ Line 90: / Line 90: @@
 input_dir=fastq
 output_dir=bam
-reference="/mnt/db/genomes/homo_sapiens/GRCh38.p14/bwa_mem_0.7.17-r1188/GCF_000001405.40_GRCh38.p14
+reference="/mnt/db/genomes/homo_sapiens/GRCh38.p14/bwa_mem_0.7.17-r1188/GCF_000001405.40_GRCh38.p14_genomic.fna"
-_genomic.fna"
 threads=10