I mapped my mate-pair data against inverted chromosome 9 sequence in an attempt to find a few large inversions (1 million base pairs+) that may have resulted from equally large deletions.
Steps I took:
1) Downloaded the human chr9.fa from UCSC Genome Browser.
2) reversed the sequence with a C program that reads the file backwards and writes into a new file.
3) I called the new file chr9inv.fa. I changed the beginning of the file from >chr9 to >chr9inv
4) I then used this file as a reference for BWA-MEM alignment on Galaxy servers.
Very few reads were aligned, and the ones that were were not properly aligned. I am not sure why.
Does BWA algorithm have issues when aligning with very large deletions in the genome? I may have done some error that I am not aware of. Any ideas?