search

MariaNattestad / Assemblytics

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.
http://assemblytics.com
MIT License
135 stars 28 forks source link

Bed file coordinate system #42

Open agolicz opened 2 years ago

agolicz commented 2 years ago

Hi, I have started using Assemblytics lately and I am trying to understand the .bed file coordinates. Are they the standard 0-based half open?

Agnieszka

MariaNattestad commented 2 years ago

I think so, but it’s been a long time, so I’m not sure. I recommend checking it, e.g. by looking at one of the smaller examples, which should also help you see what it’s doing.

On Thu, Nov 4, 2021 at 9:09 AM Agnieszka Golicz @.***> wrote:

Hi, I have started using Assemblytics lately and I am trying to understand the .bed file coordinates. Are they the standard 0-based half open?

Agnieszka

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/MariaNattestad/Assemblytics/issues/42, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB4W4PL2PU3DYSUO6T42JL3UKKV47ANCNFSM5HL2FZHA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

agolicz commented 2 years ago

Thanks. That's where my question comes from. I checked a couple of examples and it looked like it is 1-based, which is more gff/vcf than bed style.