Question

BED format - scaffold

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10.0 years ago

873243 • 0

In BED file format, what is the meaning of scaffold instead of chromosome ?

Note this format spec .

BED format genome sequence • 2.7k views

ADD COMMENT • link updated 10.0 years ago by Devon Ryan 104k • written 10.0 years ago by 873243 • 0

score 2 · Accepted Answer · 2014-12-05

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10.0 years ago

Devon Ryan 104k

If you aren't dealing with a finished* genome then you won't have full chromosomes to align against...just assembled scaffolds.

*This is probably a bad word to use.

ADD COMMENT • link 10.0 years ago by Devon Ryan 104k

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What is unfinished genome ?

ADD REPLY • link 10.0 years ago by 873243 • 0

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It might be easiest to just give an example. The Sanger Institute has sequenced the genomes of a bunch of different mouse strains. Those genomes won't typically contain chromosomes, but rather 100-200 thousand contigs and scaffolds. Why? Because you're rarely able to assemble entire mammalian chromosomes from NGS data (due to repeat regions, unequal coverage, etc.). Joining these contigs/scaffolds together to make chromosomes is a somewhat long and drawn out process that requires a lot of effort (the human and mouse genomes aren't even completely finished yet...though they're good enough for most purposes).