I'm new to Bowtie2 and have been trying to run some simple alignments in Bowtie2. My current bash script looks like this:
index_path= '/path/to/index/hg19_bt2' read_path_1= 'path/to/read1.fastq.gz' read_path_2= '/path/to/read2.fastq.gz' module load gcc/6.2.0 module load bowtie2/220.127.116.11 bowtie2 -x $index_path -1 $read_path_1 -2 $read_path_2 -S bowtie2_test.sam
However, it gives me these errors: 1. For my compressed fastq files:
"cannot execute binary file"
2. For my command line input:
"-S" does not exist or is not a Bowtie 2 index
I'm not sure what is wrong with my script because I followed the Bowtie2 manual.