Conclusion - Sara-SL/GenomeAnalysis GitHub Wiki

When I started the project and wrote my project plan I had no idea of how to run any of the softwares in this project. To try and figure out how to run the different softwares and interpret the results have taken an enormous amount of time and I have therefore only had time to do the basic analyses. As I look back on my project plan I see that I had a few questions that I believed that I would be able to answer with the basic analyses but now realize that only one have been answered.

• "Is the quality of the Mnat.v1 genome comparable to that of the high-coverage bat genomes?" This is not a question that I have investigated in this studie. I have just assumed that the quality of the Mnat.v1 genome was good and compared my assembly to this genome.

• "Is Mnat.v1 a reliable substrate for subsequent genomic analyses?" Same goes for this question.

• "What gene expression differences can be involved in the morphological divergence in bat limb development?" The genes that differ between forelimb and hindlimb could be involved since the forelimb and hindlimb develops so differently but even better would be to look into the different development stages, which I have not done in this studie.

• How does the transcriptome differ in bat forelimb and hindlimb? I have found 22 genes of intresset that differ between forelimb and hindlimb. Though to keep in mind that this is just a very small subset of the whole data so there are for sure a greater variation in in bat forelimb and hindlimb than was found in this studie.

• How does the transcriptome change between the stages CS15, CS16 and CS17? I have not had time to look into this question. It would have needed a bit more R coding.

However, even tough I have not answered all the questions, I have gotten familiar with the analysis tools and can hopefully do a more extensive analysis next time.