I am a bachelor student (biomedical sciences). We are doing a Illumina sequencing task to find out a subjects heritage.
Currently, I am struggling with our alignment step and I can't manage to find the answer anywhere.
This is my code:
bowtie2 --threads 10 -x Reference/Bowtie2/homosapiens -1 trimOutput/lc_good_1.fastq -2 trimOutput/lc_good_2.fastq -S > alignmentOutput/lc.bowtie.sam
And the error messages:
Error: 0 mate files/sequences were specified with -1, but 1 mate files/sequences were specified with -2. The same number of mate files/ sequences must be specified with -1 and -2. Error: Encountered internal Bowtie 2 exception (#1) Command: /cm/shared/apps/bowtie2/2.4.2/bin/../src/bowtie2-2.4.2/bowtie2-align-s --wrapper basic-0 --threads 10 -x Reference/Bowtie2/homosapiens -S -1 -2 trimOutput/lc_good_2.fastq trimOutput/lc_good_1.fastq (ERR): bowtie2-align exited with value 1
I have read the bowtie2 -help page a hunder times but can't seem to find the solution. Any help is much appreciated!
This is the first time I'm working with a programming language so use simple words in your response 🙂