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BoevaLab / FREEC

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
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Make graph error #132

Closed Gon1976 closed 1 year ago

Gon1976 commented 1 year ago

Hi, I use FREEC to plot ploidy in my genome assembly (freec -conf config.txt) After run freec and obain ratio.txt file I try to make the graph using: cat makeGraph2.0.R | R --slave --args JJ.bam_ratio.txt

After the png files were created, I observe the same "chromosome" repeated 13 times, but my ratio.txt file have information for 481 contigs (chromosomes) but I only can view graphs for one contig repeated (attached) JJ bam_ratio txt log2

Can you see the problem? thanks

valeu commented 1 year ago

Hi, if you have unconventional chromosome names (i.e., not chr 1 ,2 ,3.. etc), you need to manually modify the script... My apologies.