Question: Bowtie Seed Length (-L) And Non-Unique Reads Mode (M=-1)
gravatar for Eric Guo
5.9 years ago by
Eric Guo60
Eric Guo60 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
alignment bowtie • 1.6k views
ADD COMMENTlink modified 5.9 years ago by Jennifer Hillman Jackson24k • written 5.9 years ago by Eric Guo60
gravatar for Jennifer Hillman Jackson
5.9 years ago by
United States
Jennifer Hillman Jackson24k wrote:
Hi Eric, The seed length is a single input value for all sequences in any particular job. If alignment are not suppressed, then all reportable hits are in the output. More about Bowtie can be found here: Best, Jen Galaxy team
ADD COMMENTlink written 5.9 years ago by Jennifer Hillman Jackson24k
Hello Eric, I apologize, but I made a mistake, please see below This is incorrect. If alignments are not suppressed, then reporting "-a" (all) is not the default. Rather, there are several 'reporting options', and they are used in combination and with 'alignment options' to achieve different output results. It is probably best to show you the documentation, so that you can compare different parameters and output they produce. Please see: Hopefully this clears up any confusion my original reply may have caused! Jen Galaxy team
ADD REPLYlink written 5.9 years ago by Jennifer Hillman Jackson24k
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