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FPC Documentation Guide  
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The latest release is FPC V9 (28 Feb 2008)

Contents:

Documentation

  • All FPC users (new and old) should read through the FPC Tutorial and the Contig display tutorial!!! These explain most of what you need to know.
  • From within FPC, help is available for most functions. You can also access this Help from the FPC help link below.
  • The FPC help is complete for all features except for the manual editing (i.e. Contig/Edit windows). These are covered in the FPC V4 Manual.
  • Send us email with questions to fpc@agcol.arizona.edu We answer ALL questions immediately. We also really like to hear your suggestions. And please, if you find a bug, please let us know.

    Documents Purpose Demo Files
    FPC Tutorial (.doc) or
    FPC Tutorial (.htm)     		How to use the salient features of FPC.
    (Note - htm is output of Word, and a bit sloppy)     		demo.tar.gz.
    Contig display tutorial How to display contigs exactly how you want to see them.. ctgdemo.tar.gz
    MTP tutorial Using the Minimnal tiling path (MTP) function. mtpdemoV2.tar.gz
    BSS tutorial Blast some sequence against sequence associated with the map.. bssdemoV2.tar.gz
    Sequence track tutorial Align and analyze draft sequence assemblies. seqdemo.tar.gz
    HICF tutorial Using FPC with HICF (High Information Content Fingerprints). hicf_auto.tar.gz
    FPC help Available from within FPC and from here. n/a
    FPC V4 Manual Original documentation - has not been updated since V4 n/a

    The following three sections cover some information not in the Tutorials.

    File formats

    Filtering fragments

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    It is possible to filter bands from clones by entering a Vector file in the Configuration window. This file contains a list of clone types and the band values which are to be removed. Enter the vector file by selected configure on the main menu, and select Vector file and it will pop up a menu asking for the file name (note, you can't type directly into the gray box). The list of valid clone types is:- 

    bacfilter
pacfilter
yacfilter
cosmidfilter
fosmidfilter
    If any other name is used then it is used for ALL other clones. Example vector file: 
    pacfilter
111
222
333
444
    Then the first occurrence of these bands within the tolerance would NOT be added to fpc for any PAC. i.e. if a PAC had bands {111, 150, 225, 331, 443 and 445} with a tolerance of 7, then bands 111, 225, 331 and 443 would not be added to fpc. So only bands 150 and 445 would be added. In version FPC 3.2.1, the option has been added to divide your clone types by their second character. The first character is already used to define the clone type (see A.2 of manual). So filtering can be done on sub classes of clones, i.e. 
    pacfilter
111
222
333
444
pacfilter
*A
555
666
777
888
pacfilter
*J
999
1011
1111
    So what this does, is that all PACs with the second character A in their name will use the bands 555, 666, 777, 888 for filtering. All PACs with the second character J will use 999, 1011, 1111 for filtering and finally all Pacs without A or J as the second character will use 111, 222, 333, 444 for filtering. Please NOTE that the character assignment is case sensitive. So by putting *C after the clonetype you can set a different set of filter bands for that clonetype if they match C with the second character of the clones name. NB The '*' must go before the second character when defining a subtype.

    Framework

    A framework marker can be marked as 'F' for a well ordered framework, or 'P' for a partial ordered Placement. The following examples cover the possiblities accepted by FPC, where the first column is the marker name, second column is the chromosome/linkage group, third column is the location on the chromosome, and the fourth column is 'F' or 'P'. 
    Map "Demo"
Label "Chromosome"
Abbrev "Chr"
J8     X       1.1     P
A10    4       1.0     F
B13    4       1.3     P
A01    X       0.1     F

Map     "Demo"
Label   "Chromosome"
Abbrev  "Chr"
A01     2.1     0.1     F
A07     2.2     0.7     F
B13     1.1     1.3     P
C24     1.1     1.3     P
D57     3.1     5.8     F

Map     "Demo"
Label   "Chromosome"
Abbrev  "Chr"
A01     2p1     0.1     F
A05     2p1     0.1     F
A07     2q2     0.7     F
B01     1p1     1.0     F
C24     1p1     1.3     P
J130    Xp1     9.7     F

Map     "Demo"
Label   "Chromosome"
Abbrev  "Chr"
A01     2p1.10  0.1     F
A05     2p1.11  0.1     F
A07     2q2.1   0.7     F
B01     1p1.2   1.0     F
B13     1p1.2   1.3     P
C24     1p1.2   1.3     P

Map "Demo"
Label "Linkage Groups"
Abbrev "Lg"
A01     A       0.1     F
A05     A       0.1     F
A07     A       0.7     F
A10     C       1.0     F
B01     C       1.0     F
B13     C       1.3     P

Map "Demo"
Label "Linkage Groups"
Abbrev "Lg"
A01     A.1     0.1     F
A05     A.1     0.1     F
A07     A.1     0.7     F
A10     C.22    1.0     F
B01     C.10    1.0     F
B13     C.11    1.3     P

    V7 file format changes

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    FPC file

    • In the fourth line of the header, the fields 'Label' and 'Abbrev' have been added to accomodate different frameworks. The text after 'Label' determines the type of framework (Chromosome, Linkage-group, etc.), while 'Abbrev' is an abbreviation of the 'Label'.
    • In the 'Markerdata' section of the file, the 
      Global_position %7.1f [Frame]
      line has been replaced with the two lines 
      Anchor_bin "%s"
      and 
      Anchor_pos %.1f [F|P]'
      Previously, the Global_position implicitly contained both the chromosome and cM position of the anchor. This imposed a cM position limit of 999.9. With chromosome (Anchor_bin) and cM position (Anchor_pos) split, this limit has been lifted. It also allows frameworks other than chromosome to be used.
    • The 'anchor' line has been removed from Markerdata entries, as it was redundant.
    • A 'Pos' field has been added to the 'Contigdata' entries, which gives the cM position of the contig along its anchor bin, if it has been assigned.

    Format changes to the framework file

    • A header has been added: 
      Map "%s"
Label "%s"
Abbrev "%s"
      The 'Map' field identifies the framework, the 'Label' and 'Abbrev' are the values described above.
    • Anchor entries have changed. The old entry 
      "R687";"Rice";1000.0;Frame
      has become 
      R687            1        0.0     F
      This allows the usage of several types of frameworks, as described in ___. Translating old framework files into the new format is handled automatically by FPC.

    Format changes to the .fpp file

    The display preference file format has completely changed to accomodate the new contig display. Old files are no longer useful, as they apply only to the old contig display. This file is written by FPC, so the user should not need to edit it.

    Compiling V8.9 and before on Mac OSX

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    Install X11 package from Apple.

    Install glib-1.2.10.pkg, libdl.pkg, gtk-1.2.10.pkg and libintl.pkg, from macosx.forked.net or other source.

    If printing is desired the imlib must be installed. Imlib is listed at macosx.forked.net but the link was broken as of 8/14/05. If imlib has been installed, then it should be enabled in the build by removing "-DNO_IMLIB" from the Darwin makefile w/wmake/DARWIN_DEF.

    Set ACEDB_MACHINE environment variable to DARWIN.

    Type "make" in the top-level fpc directory.

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    Last Modified Wednesday April 09, 2008 11:31 AM and 31 seconds