Analyzing studies

• A study directory, like a gel directory, contains subdirectories the "input/", "display/", and "ouput/".
• The input files for a study are "settings" and "layout". A study's "settings" file is similar to a gel's "settings" file except for the gel-specific section A study's "layout" file, on the other hand, simply consists of a list of the nicknames of the gels that are in the study.
• Any program that processes a gel can also be used to process a study. For example, calling allele_call on a study has the advantage of doing the analysis (e.g. binning) across all the gels in the study.

View families

However, note that FAST-MAP does not make use of any pedigree information in genotyping -- the alleles are called solely based on the electrophoretic data. In a future version of FAST-MAP, we will provide Mendelian inheritance checking functionality and flagging the suspect genotypes that failed the inheritance constriants.

Running FAST-MAP on a Macintosh

Creating "layout" from ABI sample files

Old programs with new names

• allele_results previously known as "allele_output". The user can now sort the genotypes by sample names (for haplotypes) or by markers. In a study's "output/" directory, the ".results" file consolidates all the genotypes from all the gels.
• allele_printout previously called "allele_hardcopy".
• reset_now previously called "reset_gel", "reset_panel", and "reset_size_std".

Obsolete programs

Improved interface

Changed user file formats

• nicknames We have added a third column "type" in "nicknames" to allow specification of nicknames for the different FAST-MAP objects (gel, study, matrix, sample).
• preferences The "preferences" file has been completely revamped. We are shipping a new preferences file in the "docs/" directory called "demo.preferences" which the user can copy into the "user/" folder and modified accordingly.
• settings The gel's "settings" file has also been re-organized.

Pharmacia data