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ny-shao / ngsplot_related

ngs.plot is a useful visualization utility in the analysis of NGS data. Here are some scripts useful for the application of ngs.plot in the daily analysis.
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command line for plotting multiple BAM files along with the configuration file #1

Closed amitpande74 closed 9 years ago

amitpande74 commented 9 years ago

Hi,

I want to plot 2 BAM files in my region of interest and the example given in the config.example.txt file is not very clear to me:

If you want to specify the gene list as "genome", use "-1".

Use TAB to separate the three columns: bam filegene listtitle

"title" will be shown in the figure's legend.

hesc.H3k4me3.1M.bam -1 "H3K4me3" hesc.H3k27me3.1M.bam -1 "H3K27me3"

Could you kindly tell me the command line argument ? I had used $NGSPLOT/bin/ngs.plot.r -G hg19 -R bed -E HepG2-longRNA-intron-enhancer.bed -C sorted.H3k36.bam:sorted.RNAPII.bam -O H3K36_RNAPII_HepG2.longRNA -T H3K36_RNAPII_HepG2.longRNA -FL 300 -D refseq

but it does not seem to work...Do I have to make a separate config file for this and if so what should be the command for drawing the plots.

regards, Amit.

ny-shao commented 9 years ago

Sorry Amit, I just found your issue. Please refer to this page. Yes, you need a config file, and use the command like this:

$NGSPLOT/bin/ngs.plot.r -G hg19 -R bed -E HepG2-longRNA-intron-enhancer.bed -C config.txt -O H3K36_RNAPII_HepG2.longRNA -FL 300 -D refseq