Question: When I use sequenza to call CNV for WES,Error pops out.
0
gravatar for zhaolianhe1992
3.7 years ago by
China
zhaolianhe199220 wrote:

I had actually tried to run sequenza.extract on seqz.data but receive an error:

 

> test <- sequenza.extract(seqz.data) Error in pipe(paste("gzip -d -c", file, "| cut -f 1,6,10")) : invalid 'description' argument

 

Can anyone explain this to me in a bit further detail? Is there just something wrong with my data files or am I just making a poor assumption on what sequenza is actually doing? If sequenza.extract(data.file) is correct for real data then what purpose does the GC normalization steps serve? 

 

Thank you

cnv sequenza • 1.6k views
ADD COMMENTlink modified 3.0 years ago by Q.S.Yang0 • written 3.7 years ago by zhaolianhe199220
1
gravatar for favero
3.5 years ago by
favero10
Denmark
favero10 wrote:

Hi, soory I naven't seen this until now!

 

You probably need  to use Rtools (which include a set of common unix command for windows to run within R)

Look here:

https://cran.r-project.org/bin/windows/Rtools/

 

 

ADD COMMENTlink written 3.5 years ago by favero10
0
gravatar for Q.S.Yang
3.1 years ago by
Q.S.Yang0
China
Q.S.Yang0 wrote:

hi,have you solved the problem?

ADD COMMENTlink written 3.1 years ago by Q.S.Yang0
0
gravatar for Q.S.Yang
3.0 years ago by
Q.S.Yang0
China
Q.S.Yang0 wrote:

gz1 <- gzfile(“sample.seqz.gz","w” )

write.table(seqz.data, gz1, col.names = T, row.names=F, sep = “\t”, quote = F)

close(gz1)

gc.stats <- gc.sample.stats(“sample.seqz.gz", gz=FALSE)

This can solve the same problem.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Q.S.Yang0
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