command line for plotting multiple BAM files

[GoogleCodeExporter]

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 file<TAB>gene list<TAB>title
# "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.

Original issue reported on code.google.com by amitpand...@gmail.com on 23 Sep 2014 at 10:20

[GoogleCodeExporter]

You need to use the "HepG2-longRNA-intron-enhancer.bed" in your configuration 
file, so that it looks like this:

hesc.H3k4me3.1M.bam HepG2-longRNA-intron-enhancer.bed   "H3K4me3"
hesc.H3k27me3.1M.bam    HepG2-longRNA-intron-enhancer.bed   "H3K27me3"

got it?

Original comment by shenli.sam on 24 Sep 2014 at 3:36

• Changed state: Done
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• Removed labels: Type-Defect

[GoogleCodeExporter]

Thanks a lot!
But my question has still not been answered- what becomes of the command
line?
See for using your region of interest it has to be flagged like -R bed -E
my regions.bed,followed by the other flags.
My question is if a configuration file is being used then does it become
like this :
$NGSPLOT/bin/ngs.plot.r -G hg19 -R bed -E HepG2-longRNA-intron-enhancer.bed
-C my configuration file.txt or simply $NGSPLOT/bin/ngs.plot.r -G hg19 -C
my configuration file.txt ? and where exactly does the use "-1" flag fit in
which has been explained in the config.example.txt file.

Original comment by amitpand...@gmail.com on 25 Sep 2014 at 2:57

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[GoogleCodeExporter]

Just answered your question in another post.

Original comment by shenli.sam on 25 Sep 2014 at 7:57

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