User:Lindenb/Notebook/UMR915/20100810

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belgium

recuper les noms des HC

 gunzip -c 454HC*.gz | egrep GK | cut -d ' ' -f 1 | sort | uniq > hc_names.txt
 gunzip -c 454Reads.fna.gz | sed -e '/^>/s/[ ].*//' -e  '/^>/s/$/#/' | tr -d "\n" | tr "#" "\t" | tr ">" "\n" | fgrep -f hc_names.txt | awk '{printf(">%s\n%s\n",$1,$2);}'  > hc_sequences.fa
 grep ">" hc_sequences.fa | wc -l
 35407
 wc -l hc_names.txt 
 35407 hc_names.txt

blat

 export MACHTYPE=x86_64
  ~lindenb/bin/x86_64/blat -t=dna chrX1andX2.2bit hc_sequences.fa stdout  | gzip > hq_chrX1andX2.blat.gz