cgi-bin/content/fish.pl

   1 use strict;
   2 use CXGN::Page;
   3 my $page=CXGN::Page->new('my page','marty');
   4 $page->header("SGN FISH submission guidelines", "SGN FISH Submission Guidelines");
   5 print qq|<div>
   6 <p>This document describes what we at SGN are prepared to accept for FISH
   7 experiment data. Please <a href="http://sgn.cornell.edu/tools/contact.pl">contact us</a> if you have any questions about these guidelines.</p>
   8
   9
  10 <p>When submitting spreads, the preferred folder layout looks like this:</p>
  11
  12 <pre>&lt;chromosome arm&gt;/&lt;BACS on arm&gt;/&lt;spreads for BAC&gt;/&lt;files for spread&gt;</pre>
  13
  14 <p>For example, a single spread for a BAC on chromosome 11's long arm would
  15 be:</p>
  16
  17 <pre>
  18   Tomato_11Q/
  19   Tomato_11Q/BAC_323E19/
  20   Tomato_11Q/BAC_323E19/Spread_127/
  21   Tomato_11Q/BAC_323E19/Spread_127/127_composite.jpg
  22   Tomato_11Q/BAC_323E19/Spread_127/127_phase.jpg
  23   Tomato_11Q/BAC_323E19/Spread_127/127_fluorescence.jpg
  24 </pre>
  25
  26 <p>Other spreads for BAC 323E19 would be beside Spread_127 in the
  27 BAC_323E19 folder, other BACs on Tomato's 11Q arm would be beside
  28 BAC_323E19 in the Tomato_11Q folder, and BACs on other chromosome arms
  29 would be in folders beside Tomato_11Q.</p>
  30
  31 <p>The "Spread" IDs above are arbitrary, but it's best if the submitter
  32 uses different IDs for each spread, across their entire FISHing project
  33 (we assume that the lab already uses unique identifiers for their
  34 experiements, so we can just use those identifiers, for simplicity).</p>
  35
  36 <p>Each spread's folder must have at least the 3 image files.  We'll also
  37 store any additional per-spread datafiles beside the JPGs in the
  38 Spread_NNN folders.</p>
  39
  40 <p><em>Note</em> If possible, when multiple BACs occur in the same
  41 spread, make two distinct folders with a copy of each image in each
  42 folder (e.g., have two folders "Spread_15" and "Spread_16", rather
  43 than putting the images in a single folder called
  44 &quot;Spreads_15_and_16&quot; or something).</p>
  45
  46 <p>For each upload of several spreads, a single spreadsheet with at
  47 least the following columns (columns of other data will be ignored):</p>
  48
  49 <pre>
  50   BAC ID      Spread   BAC % from kc
  51   ------      ------   -------------
  52   323E19       127       86.99
  53   323E19       128       87.73
  54   323E19       129       88.27
  55   323E19       130       90.60
  56   323E19       131       90.58
  57   323E19       132       90.01
  58   323E19       133       86.37
  59   323E19       134       84.70
  60 </pre>
  61
  62 </div>|;
  63 $page->footer();