Bioinformatics analysis

Bioinformatics analysis is made in three steps:

1. trimming of unwanted sequences (basically anything behind the NlaIII or DpnII sites).
2. alignment to the yeast genome
3. determination of the precise transposon insertion site and counting of the number of sequencing read per transposon
4. output of a BED/WIG file for visualization

Steps 1-2 are made in the CLC genomics workbench using a workflow, steps 3-4 are performed in matlab.

The workflow is summarized below (hover on the objects for information)

Any effort of the community to perform these steps using freely available and open source software are welcome. Please contact us through the forum if you have developed a better way to perform these steps.

Once these steps have been performed, the resulting bed and wig files can be uploaded to the genome-browser.

More analyses can be performed in matlab