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--- archive:bioinformatic_tools:gs_de_novo_assembler [2010/04/24 15:36]
karplus replaced -noace by -nobig and added explanations
+++ archive:bioinformatic_tools:gs_de_novo_assembler [2010/04/24 15:48]
karplus Put -rst 0 back in, with explanation
@@ 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 -nobig .
+runProject -e 50 -nobig -rst 0 .
 </code>
 Of course, different sff files will be used on different runs.
@@ Line 56: / Line 56: @@
 The -nobig parameter suppresses the generation of big output files.
+The -rst 0 parameter (repeat score threshold) says that a read should be labeled uniquely mapped if its best hit scores >0 more than the next best (the default value is 12, which means that a lot of hits get labeled as repeats, even though they can distinguish between similar repeat regions).
 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
@@ Line 71: / Line 73: @@
 addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ01.sff
 addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ02.sff
-runProject -e 50 -nobig .
+runProject -e 50 -nobig -rst 0 .
 </code>

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