I have two questions regarding alignment using Bowtie:
1. Is there a way to set the Seed Length (-l) to the full length of each read
instead of using a single Seed Length for all reads?
2. When using m = -1 mode (Suppress all alignments for a read if more than n
reportable alignments exist (-m): OFF), will a read be randomly assigned to one
of the alignment positions in the genome? Or, will all the alignments for one
single read be reported in the final output .bam file.
Thanks in advance for your help.
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