Differences

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--- archive:bioinformatic_tools:gs_de_novo_assembler [2010/04/16 22:23]
karplus removed extraneous signature
+++ archive:bioinformatic_tools:gs_de_novo_assembler [2010/04/20 14:17]
karplus Added warning about non-serial conting numbering, added -noace
@@ Line 49: / Line 49: @@
 addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ01.sff
 addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ02.sff
-runProject -e 50 .
+runProject -e 50 -noace -rst 0 .
 </code>
 Of course, different sff files will be used on different runs.
-A Makefile that illustrates the use of the SunGrid to avoid running on the head node is shown in /campusdata/BME235/assemblies/Pog/newbler-assembly1/Makefile
+A Makefile that illustrates the use of the SunGrid to avoid running on the head node is shown in /campusdata/BME235/assemblies/Pog/newbler-assembly2/Makefile
+Note: earlier versions of Newbler provided serially numbered contigs, but version 2.3 seems to skip numbers rather arbitrarily, so that the range of the numbers is larger than the size of the set of contigs.  Look at the counts (in assembly/454NewblerMetrics.txt) or run a program to count the contigs, rather than relying on the largest contig number.
 == Mapping to existing genome ==
@@ Line 65: / Line 67: @@
 addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ01.sff
 addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ02.sff
-runProject -e 50 .
+runProject -e 50 -noace -rst 0 .
 </code>

Banana Slug Genomics