hoangtn / cnvrd2 Goto Github PK

I am trying to use a different reference genome for the correctGC rather than the default human reference genome UCSC hg19 . I have looked through the pdf manual which says to do so I have to supply my own reference genome. How do i that? There doesn't seem to be a clear input command for in the CNVrd2 function. Also what is the file format for the reference genome/how did you compile your reference genome?

Hi,
when using the countReadWindow, an issue comes up with EOF marker absent. My bam file isn't truncated and I assume it's an issue with older versions of samtools, is there any way to 'turn-off' the check for EOF marker in your appealing CNVrd2 tool?

Many thanks
objectCNVrd2=new('CNVrd2',windows=1000,chr='chr17',st=6620000,en=8540000,dirBamFile='//cronos.irt.univ-nantes.prive/EQ10_U892/NGS_Exome_Seq/BAM_hMCLs/',genes=c(6623844,8538743),geneNames='TP53')
readCoundMatrix=countReadInWindow(objectCNVrd2)

Reading file: 20161102_Nan7_final.bam
=============================================
1 bam files were read
=============================================
Error in apply(readCountMatrix, 2, function(x) ifelse(is.infinite(x), :
dim(X) must have a positive length
De plus : Warning messages:
1: In dir.create("TempAll") : 'TempAll' existe déjà
2: In doTryCatch(return(expr), name, parentenv, handler) :
[bam_header_read] EOF marker is absent. The input is probably truncated.