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SeqShop: Analysis of Structural Variation Practical, December 2014 (view source)

Revision as of 10:31, 10 December 2014

154 bytes added ,  10:31, 10 December 2014
→‎Running GotCloud/GenomeSTRiP Metadata Pipeline
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In principle, the metadata can be created from the input BAM files by running the following command
 
In principle, the metadata can be created from the input BAM files by running the following command
−
  perl ${GC}/bin/genomestrip.pl -run-metadata --conf ${SS}/gotcloud.conf --numjobs 2 --base-prefix ${SS} --outdir ${OUT}
+
  computerc.args.list
 +
cpt
 +
depth
 +
depth.args.list
 +
depth.dat
 +
gcprofile
 +
gcprofiles.list
 +
gcprofiles.zip
 +
genome_sizes.txt
 +
isd
 +
isd.dist.args.list
 +
isd.dist.bin
 +
rccache
 +
rccache.bin 
 +
rccache.bin.idx 
 +
rccache.list 
 +
rccache.merge 
 +
spans 
 +
spans.args.list
 +
  spans.dat
   −
'''WAIT!!!!! DO NOT RUN THIS COMMAND, because it will take ~50 minutes to finish'''.
+
 
 +
'''WAIT!!!!! DO NOT RUN THIS COMMAND, because it will take >1 hour to finish'''.
    
Instead, let's look what the output would have looked like.
 
Instead, let's look what the output would have looked like.
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/12295"

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