Question

Excavator - Error in JointSegIn

0

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9.4 years ago

mangfu100 ▴ 800

Hi.

I ran EXCAVATOR that detects copy number variations.

but, I was encountering some errors and I couldn't solve it.

excavator cnv • 1.9k views

ADD COMMENT • link updated 2.2 years ago by Ram 43k • written 9.4 years ago by mangfu100 ▴ 800

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Hi, I changed the title of your question to be more specific.

ADD REPLY • link 9.4 years ago by Giovanni M Dall'Olio 28k

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Hi,

could you found how to resolve this issue ?

I have the same problem.

Thanks

ADD REPLY • link updated 2.2 years ago by Ram 43k • written 9.1 years ago by jp.of.mars • 0

score 1 · Answer 1 · 2017-06-30

1

Entering edit mode

6.8 years ago

alexandre.atkinson ▴ 10

Hi,

It's an old post, but I found it with google. On this post, Alberto recommend to remove overlapping coordinate in bed: https://sourceforge.net/p/excavator2tool/tickets/1/

So I ran:

sort -k1,1 -k2,2n mybedfile.bed | bedtools merge > mybedfile_merged.bed

ADD COMMENT • link 6.8 years ago by alexandre.atkinson ▴ 10