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Old 07-09-2011, 11:36 AM   #12
jflores
Junior Member
 
Location: Mexico

Join Date: Mar 2011
Posts: 7
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Hi Tonio,

You can plot specific coordinates and try to infer from that if your gene of interest has or not gain/loss of copies.

Script :
samtools view Patient_test/Parsed_X/chr17.fa/bam/sorted.bam | perl -lane 'print "$F[2]\t$F[3]"' > test.hits
samtools view Patient_ref/Parsed_X/chr17.fa/bam/sorted.bam | perl -lane 'print "$F[2]\t$F[3]"' > ref.hits

perl cnv-seq.pl --test test.hits --ref ref.hits --genome chrom17

data <- read.delim("test.hits-vs-ref.hits.log2-0.6.pvalue-0.001.minw-4.cnv"))
plot.cnv.chr(data, chromosome=NA, from=NA, to=NA)

... For more options about plotting using CNV-seq you can have a look at the cnv.R file

Regards,

Rodrigo
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J. Rodrigo Flores
jflores@lcg.unam.mx
Center for Genomic Sciences, UNAM, Mexico
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