Version Differences for HGAP

-

Step 1 : Prepare for HGAP Protocol

+

'''Prepare for HGAP Protocol'''

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 parameter setting mostly,

+

2. Build HGAP parameters XML file : [[Media:HGAP.xml|HGAP.xml]]. we used default parameters setting mostly, and setting minSubReadLength = 50, readScore = 0.75, minLength = 50 here )

-

[Note] : Please check the "minSubReadLength", "readScore", "minLength", Genome size (Setting minSubReadLength = 50, readScore = 0.75, minLength = 50 here )

3. smrtpipe.py --params=HGAP.xml xml:input.xml (~10hr for one data set)

-								Step 1 : Prepare for HGAP Protocol
+								'''Prepare for HGAP Protocol'''
 . 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>
-. Build HGAP parameters XML file : [[Media:HGAP.xml|HGAP.xml]]. we used default parameter setting mostly,
+. Build HGAP parameters XML file : [[Media:HGAP.xml|HGAP.xml]]. we used default parameters setting mostly, and setting minSubReadLength = 50, readScore = 0.75, minLength = 50 here )
-								          [Note] : Please check the "minSubReadLength", "readScore", "minLength", Genome size   (Setting minSubReadLength = 50, readScore = 0.75, minLength = 50 here )
 . smrtpipe.py --params=HGAP.xml xml:input.xml (~10hr for one data set)