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For command line, Bowtie 3 setn is used to handle all scanning parameters. For Bowtie 2, Bowtie 3 also supports parameters by two "q" lines in regular expression form. Main scanning parameters include: startbase - specify the starting base for the offset of alignment. This is only used when searching against sequences shorter than the reference sequences. -s is used instead of -x to select a specific off-set endbase - specify the ending base for the offset of alignment. This is only used when searching against sequences shorter than the reference sequences. -e is used instead of -x to select a specific off-set readlength - specify the maximum intron length (in nucleotides) for the alignment. It is used to perform alignment for coding regions with low intron length. scorethreshold - specify the minimum scoring threshold to start the alignment for the given read. -t is used instead of -e to select a specific off-set
QStart is a module for controlling the parameters used in QStart (as part of Bowtie scripts and QStart program). It is used for setting parameters in Bowtie version 1-2 in command line, or adjust the parameters in Bowtie version 1-2 in GUI. Bowtie 3 is able to handle those parameters automatically.
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