Hi,
Does anyone know whether the BS tag in ace files reports positions
using the padded or unpadded numbering scheme?
Here's the documentation from consed 14 (at
http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt):
BS <padded start consensus position> <padded end consensus position>
<read name>
The BS line (base segment) indicates which read phrap has chosen to be
the consensus at a particular position.
If you are writing the ace file from an assembler other than phrap,
and since most assemblers do not compute the consensus this way, you
still must write BS lines for Consed's benefit. In this case, I
suggest you choose any read which matches the consensus perfectly over
the stretch of bases. There must not be any two BS lines that
intersect. Each unpadded base must be included in some BS line.
Thanks,
Ben
