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By default reverse strands are reversed and then the left is trimmed, meaning that <code>--left</code> actually trims from the right of the read in the SAM/BAM for reverse reads.
By default reverse strands are reversed and then the left is trimmed, meaning that <code>--left</code> actually trims from the right of the read in the SAM/BAM for reverse reads.
Use [[Ignore the Strand when Trimming (--ignoreStrand or --i)|--ignoreStrand/-i]] to ignore the strand information and treat forward/reverse the same.
Use [[#Ignore the Strand when Trimming (--ignoreStrand or --i)|--ignoreStrand/-i]] to ignore the strand information and treat forward/reverse the same.
===Trim Bases from the Right (<code>--right</code> or <code>--R</code>)===
===Trim Bases from the Right (<code>--right</code> or <code>--R</code>)===
By default reverse strands are reversed and then the right is trimmed, meaning that <code>--right</code> actually trims from the left of the read in the SAM/BAM for reverse reads.
By default reverse strands are reversed and then the right is trimmed, meaning that <code>--right</code> actually trims from the left of the read in the SAM/BAM for reverse reads.
Use [[Ignore the Strand when Trimming (--ignoreStrand or --i)|--ignoreStrand/-i]] to ignore the strand information and treat forward/reverse the same.
Use [[#Ignore the Strand when Trimming (--ignoreStrand or --i)|--ignoreStrand/-i]] to ignore the strand information and treat forward/reverse the same.
=== Ignore the Strand when Trimming (<code>--ignoreStrand</code> or <code>--i</code>) ===
=== Ignore the Strand when Trimming (<code>--ignoreStrand</code> or <code>--i</code>) ===
{{PhoneHomeParameters}}
{{PhoneHomeParameters}}
= Return Value =
= Return Value =
