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Old 07-08-2011, 01:43 AM   #11
tonio100680
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Location: FRANCE / Caen

Join Date: Apr 2010
Posts: 25
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Hi,

how to view the level of a gene in CNV-seq ?

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")
cnv.print(data)
cnv.summary(data)
plot.cnv(data)
ggsave("sample.pdf")
[IMG]/home/labo/Sample1.pdf[/IMG]

Regards
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