I'm fairly new to bioinformatics, and right now I'm working on a project
involving scaffolding. From a Velvet assembly I produce an AMOS file from
which I'd like to extract pairs of reads which allow contigs to be
scaffolded, as well as the distances between them. I'm under the impression
that the way to infer the distance between two reads is by measuring the
distances from each read to the ends of the contig they lie in.
Unfortunately, I can't find much documentation on how that distance is
represented by the 'off' field. If I find two reads that are related by a
FRG tag, can anyone help me with how I get the distance between them?
Thanks in advance,
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