archive:bioinformatic_tools:gs_de_novo_assembler
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| Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
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archive:bioinformatic_tools:gs_de_novo_assembler [2010/04/16 01:37] karplus bug notice, installed wrong version |
archive:bioinformatic_tools:gs_de_novo_assembler [2010/04/20 14:17] karplus Added warning about non-serial conting numbering, added -noace |
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| Line 40: | Line 40: | ||
| * stopRun | * stopRun | ||
| - | (but I haven't tested them yet --- //[[karplus@soe.ucsc.edu|Kevin Karplus]] 2010/04/15 16:02//) | + | Installed and being tested |
| - | BUG: I installed the old version...I'll have to try again with the 2.3 version. --- //[[karplus@soe.ucsc.edu|Kevin Karplus]] 2010/04/15 18:36// | + | |
| == De novo assembly == | == De novo assembly == | ||
| Line 50: | Line 49: | ||
| addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ01.sff | addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ01.sff | ||
| addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ02.sff | addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ02.sff | ||
| - | runProject -e 50 . | + | runProject -e 50 -noace -rst 0 . |
| </code> | </code> | ||
| Of course, different sff files will be used on different runs. | 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-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 == | == Mapping to existing genome == | ||
| Line 64: | Line 67: | ||
| addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ01.sff | addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ01.sff | ||
| addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ02.sff | addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ02.sff | ||
| - | runProject -e 50 . | + | runProject -e 50 -noace -rst 0 . |
| </code> | </code> | ||
archive/bioinformatic_tools/gs_de_novo_assembler.txt · Last modified: 2015/07/28 06:23 by ceisenhart
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