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Optional Parameters:
Optional Parameters:
--ignoreStrand : ignore strand information - do not reverse left/right for reverse reads
--ignoreStrand : ignore strand information - do not reverse left/right for reverse reads
--clip : soft clip the ends rather than setting to N/!
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{{PhoneHomeParamDesc}}
{{PhoneHomeParamDesc}}
If the 3rd argument a number (with no flag/option), it is the number of bases to trim from each end of the reads.
If the 3rd argument a number (with no flag/option), it is the number of bases to trim from each end of the reads.
===Trim Bases from the Left (<code>--left</code> or <code>--L</code>)===
===Trim Bases from the Left (<code>--left</code> or <code>-L</code>)===
Use <code>--left</code> or <code>--L</code> followed by the number of bases to be trimmed from the left.
Use <code>--left</code> or <code>-L</code> followed by the number of bases to be trimmed from the left.
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>)===
Use <code>--right</code> or <code>--R</code> followed by the number of bases to be trimmed from the right.
Use <code>--right</code> or <code>-R</code> followed by the number of bases to be trimmed from the right.
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>) ===
Use <code>--ignoreStrand</code> or <code>--i</code> to ignore the strand information and treat forward/reverese the same. When <code>--ignoreStrand</code> or <code>--i</code> is set, do not reverse reverse reads prior to trimming left/right.
Use <code>--ignoreStrand</code> or <code>--i</code> to ignore the strand information and treat forward/reverese the same. When <code>--ignoreStrand</code> or <code>--i</code> is set, do not reverse reverse reads prior to trimming left/right.
=== SoftClip the Ends (<code>--clip</code> or <code>-c</code>) ===
Use <code>--clip</code> or <code>-c</code> to soft clip the ends instead of setting to N/!.
When clipping:
* output is not sorted (start positions may change after soft clipping)
* soft clips already in the read are maintained or added to
** if 3 bases were clipped and 2 are specified to be clipped, no change is made to that end
** if 3 bases were clipped and 5 are specified to be clipped, 2 additional bases are clipped from that end
* if the entire read would be soft clipped, no clipping is done, and instead the read is marked as unmapped
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