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To process the EST data set, I used the following command to strip off the first column
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gunzip -c X_tropicalis_Nov_2009_all_est.gz | grep -v bin | cut -f2- > X_tropicalis_Nov_2009_all_est.psl |
Next, I sorted and created an index using bgizp and tabix:
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sort -k14,14 -k16,16n X_tropicalis_Nov_2009_all_est.psl > sorted.psl mv sorted.psl X_tropicalis_Nov_2009_all_est.psl bgzip X_tropicalis_Nov_2009_all_est.psl tabix -s 14 -b 16 -0 X_tropicalis_Nov_2009_all_est.psl.gz |
I've created a number of data files, and so my next step will be to try opening them in IGB. I also want to test whether IGB will be able to open and display the genome sequence.
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