User:Lindenb/Notebook/UMR915/20101013

20101012        Top        20101014       

Belgium

modified bomcat for handling more than one directory for the 454HC*.txt.gz stuff and added the new file for RR.

RR ask for joining result with original CSV data:

  gunzip -c XXXXunpaired_trimmed_mapping_SNP_DIP.csv.gz | tr ";" "   " | egrep '(chrXXXXX|position)'| egrep '(SNP|position)' | cut -d '        ' -f 2,8,9,10-17 | tr -d "." | tr -d '"' > ~/jeter2.txt 
  
  wc result.txt 
  352 13253 82717 result.txt

  sort -t '  ' -k 2,2 result.txt  > jeter01.tsv
  sort -t '  ' -k 1,1 jeter2.txt | uniq > jeter02.tsv
  join -t '  ' -1 2 -2 1   jeter01.tsv jeter02.tsv

Biostart/Blast

http://biostar.stackexchange.com/questions/2892

formatdb some seqs

   formatdb -n testDB -p F -i test.fa

  xjc  -httpproxy "xxxxxxxxxxxxxxx:3128" -d src -p blast -dtd "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"