Add descriptions of expected output in .bed files

dfguan / asset

assembly evaluation tool

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Add descriptions of expected output in .bed files #7

Open kkowalden opened 3 years ago

kkowalden commented 3 years ago

Hello,

I'm using your tool to evaluate assemblies produced with PacBio HiFi reads, 10x reads, and Omni-C reads.

Can you provide descriptions of the expected output columns in the various bed files?

My final punchlist bed file has only "C"s present in the final column, which I assume means "conflict". I don't have any "S", which I'm assuming means "supported".

If I knew what the upstream file fields are, I can possibly troubleshoot there.

Thanks! Kim

dfguan commented 3 years ago

Hi Kim,

C means a mis-assembled contig sequence, while S represents a mis-assembled join, i.e. two contigs were wrongly joined.

Best,

Dengfeng.