There is growing interest in using "alternative sequencing
chemistries" instead of sequencing DNA on both strands. We are
therefore planning to treat readings obtained using these alternative
chemistries in special ways within our assembly program gap4. For
example, regions covered by such readings could be counted as having
data on both strands.
Obviously this will require a change to the database (which need not
concern users), but we also need a method of supplying the information
about the type of sequencing chemistry used to gap4. One possibility
is to add a new record type to experiment files, and the simplest and
most general is to assign a non-zero number to all readings obtained
using methods that users wish to be considered as special. If it was
convenient, this information could be stored in the SCF file as well
and be added from there to the corresponding experiment file.
In the SCF file we could have a comment with code CHEM and in the
experiment file a CH record. Obviously these records will not be
obligatory and any reading reaching gap4 without a CH record will be
treated as standard data.
For example in the SCF file CHEM=1
and in the expt file
CH 1
Please send us any comments you have about this, plus the names and
references of sequencing chemistries that you would like to be
considered as special.
James Bonfield, Kathryn Smith and Rodger Staden
--
James Bonfield (jkb at mrc-lmb.cam.ac.uk) Tel: 01223 402499 Fax: 01223 412282
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
