What does -5 mean in bedtools genomecov?

arq5x / bedtools

A powerful toolset for genome arithmetic.

http://code.google.com/p/bedtools/

GNU General Public License v2.0

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What does -5 mean in bedtools genomecov? #136

Open Rhine86 opened 6 years ago

Rhine86 commented 6 years ago

help message shows that -5 mean "calculate coverage of 5' positions instead of entire interval", but I don't know what's 5' position exactly means?

ZHANG Yan

FatihSarigol commented 5 years ago

Thanks for this question! I am wondering exactly the same thing at the moment. Did you find an answer to it? I look into my bam file with tview, but the numbers genomecov -5 reports for certain positions doesn't make perfect sense to me, I can't see any pattern about what it exactly counts..

cmatKhan commented 2 years ago

I'm curious to know how this setting treats soft clipping -- is it 5' of the alignment, or the query?