Entering edit mode
9.0 years ago
zizigolu
★
4.3k
Hi
I am going to have two 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 don't 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?
