in the rRNA filtering part i am going to map the fastq reads on the rRNA sequences and keep only the reads which has not been mapped, in cmd i should type:
bowtie2 -x [name of the bowtie2-build indicized file containing the rRNA sequence] --un [name of the fastq file which will contain the UNMAPPED reads] -U [name of the fastq file containing the reads] -S [name of the .sam file that will contain the MAPPED and UNMAPPED reads]
I could not understand about --un option because i don't know which i should type instead of [name of the fastq file which will contain the UNMAPPED reads]..
is the name optional?? in typed some optional names with gz Suffix but always error