NgsCctsBuildCompleteGenomics

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(download reference genomes from CG)
(download reference genomes from CG)
Line 17: Line 17:
  
 
download reference data
 
download reference data
   cd /scratch/share/ngs/databases/completegenomics
+
   cd /scratch/share/public_datasets/ngs/databases/completegenomics
 
   qsub cg_download_36.sh
 
   qsub cg_download_36.sh
 
   qsub cg_download_37.sh
 
   qsub cg_download_37.sh
Line 27: Line 27:
 
   module load ngs-ccts/completegenomics-cgatools-1.7.1
 
   module load ngs-ccts/completegenomics-cgatools-1.7.1
 
   # list contents
 
   # list contents
   cgatools listcrr --reference ReferenceFiles build${BUILD}.crr > build${BUILD}.listcrr.out
+
   cgatools listcrr --reference ReferenceFiles/build${BUILD}.crr > build${BUILD}.listcrr.out
 
   diff build${BUILD}.listcrr.ref build${BUILD}.listcrr.out
 
   diff build${BUILD}.listcrr.ref build${BUILD}.listcrr.out
 
   # extract some sequence
 
   # extract some sequence
 
   cgatools decodecrr --reference ReferenceFiles/build${BUILD}.crr --range chr16:10000000-10000050
 
   cgatools decodecrr --reference ReferenceFiles/build${BUILD}.crr --range chr16:10000000-10000050

Revision as of 22:47, 29 August 2013

Binary install of Complete Genomics Analysis Tools

Source http://sourceforge.net/projects/cgatools/files/

1.7.1 (2013-08-29)

 # binary download
 cd /share/apps/ngs-ccts/downloads
 wget http://sourceforge.net/projects/cgatools/files/1.7.1/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz/download
 cd ..
 tar xzvf downloads/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz
 # create module file
 emacs /share/apps/ngs-ccts/modulefiles/completegenomics-cgatools-1.7.1.5
 # edit, edit edit

download reference genomes from CG

download reference data

 cd /scratch/share/public_datasets/ngs/databases/completegenomics
 qsub cg_download_36.sh
 qsub cg_download_37.sh


validate downloaded .crr

 BUILD=36
 cd /scratch/share/ngs/databases/completegenomics
 module load ngs-ccts/completegenomics-cgatools-1.7.1
 # list contents
 cgatools listcrr --reference ReferenceFiles/build${BUILD}.crr > build${BUILD}.listcrr.out
 diff build${BUILD}.listcrr.ref build${BUILD}.listcrr.out
 # extract some sequence
 cgatools decodecrr --reference ReferenceFiles/build${BUILD}.crr --range chr16:10000000-10000050
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