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• 6.1 Genome indexing for bowtie
  cd /ibers/ernie/home/vpl/zebrafish/bt2Index
  4 KB (726 words) - 13:12, 11 May 2016
• 6.2 Read mapping using tophat
  cd /ibers/ernie/home/vpl/zebrafish
  5 KB (800 words) - 15:55, 12 February 2016
• 6.3 Transcriptome reconstruction and expression using cufflinks
  cd /ibers/ernie/home/vpl/zebrafish -b /ibers/ernie/home/vpl/zebrafish/bt2Index/chr12.fa \
  8 KB (1,281 words) - 10:58, 18 February 2016
• 9.1 Genome indexing for bwa
  bwa index -p danRer10 /ibers/ernie/scratch/vpl/zebra_fish/bwaMapping/danRer10.fa '''path to genome''': /ibers/ernie/scratch/vpl/zebra_fish/bwaMapping/danRer10.fa
  2 KB (356 words) - 15:59, 20 February 2016
• 9.2 Read mapping using bwa
  cd /ibers/ernie/scratch/vpl/zebra_fish/bwaMapping
  2 KB (265 words) - 16:07, 20 February 2016
• 9.3 SNP calling using varscan
  $ samtools mpileup -f /ibers/ernie/scratch/vpl/zebra_fish/bwaMapping/danRer10.fa 2cells.sorted.bam > 2cells.pileup cd /ibers/ernie/scratch/vpl/zebra_fish/bwaMapping
  3 KB (448 words) - 14:40, 25 February 2016
• 8. De novo assembly with Velvet
  cd /ibers/ernie/scratch/vpl/zebra_fish
  4 KB (543 words) - 16:30, 22 February 2016