User:Lindenb/Notebook/UMR915/20101019

From OpenWetWare
Jump to: navigation, search
Owwnotebook icon.png

20101018        Top        20101020       


Mediawiki

allow file permission for upload

  sudo chown -R apache: images

Exome Explorer

working on a BDB based solution for exploring the exome data.

inserting varscan data computed last week:

  for I in 1 ...
  do
    echo $I
    java -jar exomeexplorer.jar -dataset Brs -p varscan -sample-id ${I} ~/tmp/varscan_pileup2indel_${I}.tsv.gz
  done
  
  for I in 1 ...
  do
    echo $I
    java -jar exomeexplorer.jar -dataset Brs -p varscan -sample-id ${I} ~/tmp/varscan_pileup2snp_${I}.tsv.gz
  done

size:

  du  -h ${BDB_HOME} 
  913M

export to PPH2

  java -jar /home/lindenb/src/code915/dist/exomeexplorer.jar -dataset BRUGADA -p export-pph2 | grep -v random | cut -d ':' -f 1 | uniq -c
 
282162 chr1
167581 chr10
133953 chr11
124379 chr12
 43800 chr13
 70688 chr14
100045 chr15
132123 chr16
133673 chr17
 52556 chr18
131116 chr19
206142 chr2
 60017 chr20
 47914 chr21
 54993 chr22
136773 chr3
178806 chr4
113768 chr5
125006 chr6
141257 chr7
 94362 chr8
118050 chr9
   489 chrM
 70106 chrX
106560 chrY

same number as in varscan ?

gunzip -c ~/tmp/varscan_pileup2snp_*.gz | grep -v random | grep -v Chrom | cut -d ' ' -f 1,2,3,4 | sort | uniq | cut -d '   ' -f 1 | sort | uniq -c
282162 chr1
167581 chr10
133953 chr11
124379 chr12
 43800 chr13
 70688 chr14
100045 chr15
132123 chr16
133673 chr17
 52556 chr18
131116 chr19
206142 chr2
 60017 chr20
 47914 chr21
 54993 chr22
136773 chr3
178806 chr4
113768 chr5
125006 chr6
141257 chr7
 94362 chr8
118050 chr9
   489 chrM
 70106 chrX
106560 chrY

ok same