Gmap tutorial from Sylvia Martinelli, Sanger Centre. 250797. ============================================================== This tutorial uses the worm database available from ftp.sanger.ac.uk/pub/acedb/Celegans/ in its full version or from Sylvia Martinelli in a smaller version which has the Genetic Map for Chromosome IV and the Sequence-map. This is in ftp.sanger.ac.uk/pub/sylvia/exprace.tar.Z. There are other tutorials in the same directory course97.tar.Z for curators. MAP TOOLS : HIGHLIGHTING =========================== 1. get a map of chromosome IV and preserve it. On the class window, select Locus let*. Go back to the map and using the Highlight button's menu, Highlight selected loci in magenta. Then try the other choices on the menu; for example, highlight all the deletions with 's' in their name. PLAYING WITH GMAP CONFIGURATION AND MAKING NEW MAPS. ======================================================= With the a database to which you have write access 1. Get a map of chromosome IV. Use the top left button to move to different views (i.e. with or without rearrangements etc.) These are commonly required views in the worm community and therefore supplied with the worm data. 2. Using the same button, get menu. Looking at right hand columns : Try toggling some of buttons on and off and re-drawing the map. 3. Try moving columns up or down by selecting them and clicking on another arrow to move them to that arrow position. Redraw. 4. Use a different method of displaying intervals. This involves getting a new column definition from the left hand side by highlighting it (say Interval_JTM) then clicking on an arrow on the right hand side to interpolate it. Re_draw. 5. Make a map with just 3 different ways of displaying intervals. and a scale bar and locator and Marker_loci. 6. Save this new map-type. 7. Using the 3-interval map, configure the Interval_SRK column. On the configure window, next to Query for display, type FOLLOW rearrangement. Find a query for the colouring of objects. I have tried asking for presence of Locus mapped to this rearrangement (Locus_inside) and for a clone (Clone_inside). You could also try Deletion and Duplication as different colours. (every time you add something to the map, you should save by overwriting the previous save.) 8. Using the 3-interval map, try changing column widths. Instead of invoking the view control menu, you can go straight to configure by clicking on the column name in green at the bottom of the map. 9. Try similar things with Map Sequence-IV : adding columns, changing widths, changing queries and colours, and try saving some of these. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ NONE OF THE ABOVE ADDS ANYTHING NEW TO THE MAP, JUST RE-DRAWS EXISTING OBJECTS ATTACHED TO THE MAIN MAP OBJECTS. THE NEXT EXERCISES ADD (1) : NEW OBJECTS, (2) : NEW MAPS. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ADDING NEW OBJECTS TO AN EXISTING MAP ------------------------------------------ 10. To add new objects to the map. Look at the Map Sequence-IV text version. Sequence-IV shows the clones used for sequencing and gives a quick visual progress report. Its a very simple display to which you could add several other classes of objects. 10a. To add a column get the view control menu. To add a piece of text, try adding Derived_tags to the active column list. If you Re-draw, nothing happens, so then configure the new column. Fill in the Query (CLASS) at the top, also the Tag in the first list and try various radio buttons on the right side for their effect. Re-draw. (I used FOLLOW Clone and General_remark because the only objects contained in Map_sequence are clones and sequences). Save the view under a new name. 10b. Add a points column. Here it gets more labour intensive. The only things in the worm database with Point positions are Loci. So add a points column to the active list and then try configuring. Nothing happens however hard you try unless the Loci are listed under the Map Sequence-IV object AND they have positions on the Sequence map. I dumped out the Loci resulting from the query >?Clone Map = IV Positive_locus into rawdata/locseqmapIV.ace. I added some data to each locus which has a position on the gmap : Map Sequence-IV Position xyz. Position xyz was estimated as the mid-position of the relevant clone. This was read back in and the names of these loci were added to the Map Sequence-IV object. 10c. I also added a column to display those cDNAs on IV. The data is in cDNAonIV.ace You may need to re-calculate the map and/or Align maps at various points. ------------------------------------------------- MAKING A NEW MAP OBJECT --------------------------- 11. Its a good idea to look at the models used by the code to get an idea of what you have to specify in maps and views. You have to make a map object and a view object, put some objects under contains in the map object and give them positions relative to the scale you choose for the map object. I used clone (cosmid) B0303 with a notional length of 40000 DNA bases, centred at 20000. I used the fMap display to work out some positions for the predicted gene sequences which I have put as objects into the Contains section of the map object. I added Left and right end positions to the new map object within each sequence object. When I used the map, I added columns using view control : points and derived tags. The data I read in is in rawdata/seqb0303.map.ace. (note, B0303 is not on Sequence-map IV so I moved it to IV so that I could make a map of B0303 within a map, in the future. This has not been implemented here yet.) If you have trouble with this please email me sylvia@sanger.ac.uk. cDNAonIV.ace is on the ftp server, see top. seqb0303.map.ace ditto locseqmapIV.ace ditto