how can I feed Bowtie2 after trimming the fastaq files through trimmomatic?
The output of the trimmomatic implementation returns 4 files, which can be called let's say paired1, paired2, unpaired1 and unpaired2, and I created the index reference file idx_refile. I therefore used this kind of command:
bowtie2 -x idx_refile -1 paired1 -2 paired2 -U unpaired1, unpaired2 -S output.sam
but I got the following error:
Extra parameter(s) specified: "unpaired2"
Note that if <mates> files are specified using -1/-2, a <singles> file cannot
also be specified. Please run bowtie separately for mates and singles.
Error: Encountered internal Bowtie 2 exception (#1)
(ERR): bowtie2-align exited with value 1
How can I separate the unpaired files? the comma did not work...