Analysis 7: RNA Mapping (BWA and SAMtools) - cecilia-andersson/Genome_Analysis_Project GitHub Wiki

I used BWA-MEM and SAMtools to map the RNA reads files from each location to each bin. After indexing the bins with BWA, I ran BWA-MEM using the bin's .fa file, mapping the forward and reverse RNA reads back to each bin iteratively. I did this separately for each location, ending up with two bam files of reads mapped to each bin. Again, I didn't want heavy .sam files, so I piped through to sort and index each with SAMtools, resulting in those aforementioned bam files.

This resulted in 96 total bam files, which is one for each location for each bin.

Mapping reads to bins is essential for later analyses of expression because although genome annotation is helpful in understanding what the function of each organism could be, this does not fully describe what is actually happening in the environment. For example, without further RNA expression analysis, it would not be possible to know which organisms are producing which proteins, and at what levels. Mapping is the first step in identifying which organisms (bins) express which genes.

To think about:

• What percentage of your reads map back to your contigs? Why do you think that is?

I don't know how to get this information, but I would guess that most reads do not map back to contigs because not all contigs were placed into bins (as discussed in the binning analysis). If some of these contigs actually contained functional coding sequences and were just difficult to associate with other contigs into a bin, there may still be reads from the RNA sample associated with those unbinned contigs.