Hello. I am trying to run bowtie2.
This is directly from the Biostarhanbook.
Get reference: ACC-JQ340389 efetch -db=nuccore -format=fasta -id=$ACC >.refs/$ACC.fa $ACC
dwgsim -N 10000 $ACC.fa $ACC
index the reference bowtie2-build $ACC.fa $ACC
Run bowtie2: bowtie2 -x $ACC -1 #READ1 -2 $READ2 | samtools view -h -b | samtools sort > $ACC.bam
THEN I GET THE ERROR: (ERR): Argument expected in next token! Exiting now ...
I do not know what to make of this error and how to fix it.
Can anyone help?