Hello,
I would appreciate your input on my Whole Genome Bisulfite Sequencing (WGBS) analysis approach. I am currently analyzing changes in methylation patterns between my parent plants (P1 and P2 – different species and non-model organisms) and their F1 hybrids. While I have access to the respective genomes for P1 and P2, the P1 genome appears to be of poor quality, or our plants may differ from the published accession.
Challenges: The main challenge arises when mapping the reads from the F1 hybrids due to the high similarity between the P1 and P2 genomes, making it difficult to distinguish which genome the reads belong to.
Current Approach:
Objective: Use mismapping from P1 to P2 and vice versa to identify regions where hybrid reads are likely to mismatch.
Mapping Strategy:
- Map P1 reads to an artificial hybrid genome (P1 + P2) and extract the mismapping location
- Same for P2 reads
- Utilize the mismapping locations to mask the hybrid genome for hybrid reads mapping
Problem Encountered:
A significant number of mismappings from P1 onto the P2 part of the hybrid genome leads to 70-80% masking of the P2 genome, rendering downstream processing ineffective. Conversely, mapping from P2 to P1 results in only about 30% masking.
I am also considering an alternative approach: mapping the hybrid reads separately on the P1 and P2 genomes and excluding reads that map to both. However, this would necessitate discarding a substantial number of reads.
I would greatly appreciate any suggestions or tips for improving my mapping strategy for the hybrid reads.
Thank you!
