BWA Alignments missing regions
Hello,
I have a very short gene sequence that I have appended to my reference assembly as a "new" chromosome. I have then aligned the new assembly to a set of 101 PE Illumina reads using BWA; however I find that only the ends of this new chromosome have read mapping. There is no data in the middle.
The sequence reads do contain the gene sequences, they just don't seem to align. Any suggestions on what parameters I can tweak to get results?
Thanks for your input!
Cheers,
BW
I have a very short gene sequence that I have appended to my reference assembly as a "new" chromosome. I have then aligned the new assembly to a set of 101 PE Illumina reads using BWA; however I find that only the ends of this new chromosome have read mapping. There is no data in the middle.
The sequence reads do contain the gene sequences, they just don't seem to align. Any suggestions on what parameters I can tweak to get results?
Thanks for your input!
Cheers,
BW
