Version Differences for HGAP
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(→Hierarchical genome-assembly process)
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(→Hierarchical genome-assembly process)
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| '''Prepare data for HGAP Protocol''' <br> | '''Prepare data for HGAP Protocol''' <br> | ||
| 1. Build input XML file (detail step please refer to the [https://github.com/PacificBiosciences/SMRT-Analysis/wiki/SMRT-Pipe-Reference-Guide-v2.0#PipeInputs tutorial]) <br> | 1. Build input XML file (detail step please refer to the [https://github.com/PacificBiosciences/SMRT-Analysis/wiki/SMRT-Pipe-Reference-Guide-v2.0#PipeInputs tutorial]) <br> | ||
| - | 2. Build HGAP parameters XML file : [[Media:HGAP.xml|HGAP.xml]]. we used default parameters setting mostly, and set minSubReadLength = 50, readScore = 0.75, minLength = 50. <br> | + | 2. Build HGAP parameters XML file : [[Media:HGAP.xml|HGAP.xml]]. We used default parameters setting mostly, and set minSubReadLength = 50, readScore = 0.75, minLength = 50. <br> |
| 3. execute HGAP protocol. | 3. execute HGAP protocol. | ||
| smrtpipe.py --params=HGAP.xml xml:input.xml | smrtpipe.py --params=HGAP.xml xml:input.xml | ||
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| 3. SMRT protal will generate a reference folder under /opt/smrtanalysis/common/userdata.d/references/XXXXXX. You can copy the whole folder to your working directory, or asign the path in the Quiver.xml <br> | 3. SMRT protal will generate a reference folder under /opt/smrtanalysis/common/userdata.d/references/XXXXXX. You can copy the whole folder to your working directory, or asign the path in the Quiver.xml <br> | ||
| - | Step 3 : Prepare for Quiver | + | '''Prepare for Quiver'''<br> |
| - | 1. Build Quiver parameters XML file : Quiver protocal | + | 1. Build Quiver parameters XML file : [[Media:Quiver.xml|Quiver.xml]]. We set minSubReadLength = 50, readScore = 0.75, minLength = 50, and the others we used default value.<br> |
| - | [Note] : Please check the "minSubReadLength", "readScore", "minLength", Reference file folder path. (Setting minSubReadLength = 50, readScore = 0.75, minLength = 50 here ) | + | 2. execute Quiver protocol. <br> |
| - | 2. smrtpipe.py --params=Quiver.xml xml:input.xml | + | smrtpipe.py --params=Quiver.xml xml:input.xml |