i am going to have tow files: one sam file containing mapped and unmapped reads and another file containing just unmapped reads by --un option by this command (windows)
bowtie2-align-s.exe -x arabidopsis_genome
--un unmapped.fastq -U C:\seq\GSM575243.fasta -S eg1.sam
but i dont know for afresh file which name i should type or totally why i am facing this error: warning bowtie2-align run directly. it is recommended that you run the wrapper script "bowtie2" instead
then how i can have two separate files with --un option?