I am trying to do global alignment using bowtie2 with following command:
bowtie2 -p 4 -x bowtie_index/wu_0 wu_0_A_wgs.fastq -5 wu_0_A_wgs.bt2.sam >& wu_0_A_wgs.bt2.sam
It showed me the working of bowtie2 to generate .sam file((https://i.stack.imgur.com/lR5wI.png) but when i am checking in my present working directory, there is no .sam file
Anyone has any clue if i am making any mistake in the code