roimethstat

[lawrence ong]

Hi, 

I'm trying to use roimethstat with a region of interest file that includes various gene isoforms whose coordinates overlap. For example 

chr1	11822249	11849642	C1orf167
chr1	11837133	11839676	LOC102724659

Even after using the sort command prescribed, I've found that the roimethstat program still says that the region of interest file isn't sorted. 

Is this because the program can't deal with overlapping coordinates? Is there any way around this?

Thanks 

Lawrence

[Ben Decato]

Hi Lawrence,

When I run roimethstat with your example coordinates and an IMR90 methcounts file I have laying around, I get the following result:

 roimethstat -L test.bed Human_IMR90_chr1.meth 

chr1    11822249        11849642        C1orf167:558:551:8777:12246     0.716724        +

chr1    11837133        11839676        LOC102724659:43:40:671:850      0.789412        +

It seems to be producing the correct values. Are these the two lines that it is telling you are not sorted? Which version of methpipe are you running? Can you send me a larger snippet of both your methcounts file and regions file, as well as the command you used to sort?

Thanks,

Ben

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Benjamin Decato, Ph.D.
Computational Biology Section,
Department of Biological Sciences,
University of Southern California
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[lawrence ong]

Hi Ben, 

Thanks for getting back to me. 

I managed to get it to work. I think it was the presence of contigs and haplotype chromosomes in my roi file. 

Cheers

Lawrence 

and my other .meth file looks like