Genome Alignment

In order to do differential expression analysis of genes, we need to align the reads against a reference. The alignment software being used has to account for the type of organism being analysed. Since _M.natalensis is a eukaryote,the presence of exons and introns also needs to be taken into account.

For this purpose, Bowtie was used to create index files. Following the creation of index files, TopHat was used to align paired ended reads for all developmental combinations as listed below:

• Stage: CS15

  • Appendage: forelimb
  • Appendage: hindlimb

• Stage: CS16

  • Appendage: forelimb
  • Appendage: hindlimb

• Stage: CS17

  • Appendage: forelimb
  • Appendage: hindlimb