genebody vs. bed file coordinates

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What does the genebody option plot in the average profile?
Does it plot the coverage over the entire gene (TSS to TES including introns), 
or only within the exons?

I see a big difference when using the ngsplot 
hg19.ensembl.genebody.protein_coding.RData database and when using the same 
coordinates submitted as a  bedfile.

ngsplot version 2.41.3

ngs.plot.r -G hg19 -R genebody -C config_testlist_stranded.txt -O 
ngs41_testlist2_same -F rnaseq -SC global -L 100 -P 8 -SS opposite

config_testlist_stranded.txt:
../E_firstofpair.bam    test_list.txt    "hRRP6"
../A_firstofpair.bam    test_list.txt    "normal"

vs

ngs.plot.r -G hg19 -R bed -C config_test2_stranded.txt -O ngs41_test2_opposite 
-F rnaseq -SC global -L 100 -P 8 -SS opposite

config_test2_stranded.txt:
../E_firstofpair.bam    test2.bed    "hRRP6"
../A_firstofpair.bam    test2.bed    "normal" 

gene used is ENSG00000105708 

Thanks,

Graeme

Original issue reported on code.google.com by graeme.g...@gmail.com on 18 Mar 2015 at 3:27

[GoogleCodeExporter]

When you use "-F rnaseq", ngs.plot concatenates the coverages for exons. Of 
course, it will look different from your bed files which contain the DNA 
coordinates of TSS and TES.

Li

Original comment by shenli.sam on 20 Mar 2015 at 4:44

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[GoogleCodeExporter]

Thanks for the quick response.

Original comment by graeme.g...@gmail.com on 20 Mar 2015 at 4:52

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