# creating index :
bowtie2-build  reference_file_name.fasta  prefix_of_output_index_file

# mapping reads :
# -x path to index, only prefix needed
# -1 first file with paired end reads
# -2 second file with paired end reads
# -U files with unpaired reads
# -S output file name

./bowtie2 -x prefix_of_output_index_file \
-1 file_1P.fastq \
-2 file_2P.fastq \
-U file_1U.fastq \
-U file_2U.fastq \
-S mapping.sam

# NOTE:
# if number of reads in paired-end files is uneven, bowtiew will throw and exception
# you can get uneven number of files, when you additionally recrop one of them in SE mode of Trimmomatic
# in this case use this approach :

bowtie2 -x prefix_of_output_index_file \
-U file_1P.fastq \
-U file_2P.fastq \
-U file_1U.fastq \
-S mapping.sam