Question: Bowtie Seed Length (-L) And Non-Unique Reads Mode (M=-1)
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Eric Guo • 60 wrote:
Hi there,
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.
-Eric
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modified 6.7 years ago
by
Jennifer Hillman Jackson ♦ 25k
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written
6.7 years ago by
Eric Guo • 60
