Homework Assignment #3

Make a graph showing the variation of both female and male recombination rates across the human genome.

Step 1: Get the data. Start at the USCS Table Browser for the Mar. 2006 human assembly (hg18). For the group "Mapping and Sequencing Tracks" and track "Recomb Rate", click on "describe table schema". You'll see that there are three sources of recombination rates (decode, marshfield and genethon), and three rates for each source (average, female and male). We don't want the entire table, so set the output format to "selected fields from primary related tables" (don't send to Galaxy), then click on "get output", select the fields chrom, chromStart, decodeFemale, and decodeMale, and press "get output" again. Use your window system's Copy operation in preparation to upload it for the next application. If you have any problems with this you can type of paste the following URL into the next upload window: http://www.bx.psu.edu/courses/bx-fall09/recomb-rates.txt

Step 2: provide the recombination data to the USCS Human Genome Graphs tool for hg18. Click on the "upload" button, specify the name of data set as "recomb-rate", paste either the table of recombination rates into the window, click "submit", read the message, and click "OK".

Step 3: configure the graph. At Human Genome Graphs, press "configure" and pick: image width 800, graph height 25, graphs per line 2, and lines of graphs 2. Then press "submit". Select "recomb-rate 2" for the first graph and "recomb-rate 1" for the second graph, with whatever colors you like. The "1" and "2" after "recomb-rate" refer to the position of the desired column following the "chromosome" and "position" columns.

Step 3: send me your graph as an email attachment by noon on Saturday Sept. 12.