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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/! |
| </pre> | | </pre> |
| {{PhoneHomeParamDesc}} | | {{PhoneHomeParamDesc}} |
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| 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 |
| + | |
| | | |
| {{noeofBGZFParameter}} | | {{noeofBGZFParameter}} |