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

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


> test <- sequenza.extract( 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 • 1.8k views
ADD COMMENTlink modified 3.8 years ago by Q.S.Yang0 • written 4.5 years ago by zhaolianhe199220

hi,have you solved the problem?

ADD REPLYlink written 3.9 years ago by Q.S.Yang0
gravatar for favero
4.4 years ago by
favero10 wrote:

Hi, sorry I haven'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:

ADD COMMENTlink modified 4 months ago by RamRS26k • written 4.4 years ago by favero10
gravatar for Q.S.Yang
3.8 years ago by
Q.S.Yang0 wrote:
> gz1 <- gzfile(“sample.seqz.gz","w” )
> write.table(, 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 4 months ago by RamRS26k • written 3.8 years ago by Q.S.Yang0
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