Liftover from mm10 to CAST/PWK – Very Low Mapping Rate & Missing Chain File

Question

[daffodil]

Hi,I’m currently working on a piRNA project and trying to map annotated piRNA cluster coordinates from the mm10 reference genome to PWK and CAST/EiJ genomes.

So far, I’ve tested both CrossMap and UCSC liftOver using the available chain files:

mm10ToMm39.over.chain.gz

mm39ToGCA_001624775.1.over.chain.gz (for PWK)

But I don’t have a chain file for CAST/EiJ (e.g., mm39ToCAST_EiJ.over.chain.gz is not publicly available from UCSC)

Here’s the issue I’m facing:

My input BED12 file contains 316 piRNA cluster regions in mm10

After running liftover (either via CrossMap or liftOver), only ~2 regions are successfully mapped to PWK

The rest end up in the .unmap output

Many of my regions are large (50–600 kb), which might affect mapping

I’m trying to understand: Is the poor mapping due to region size or gaps in the PWK/CAST chain files?

Is there any way to obtain or generate a reliable CAST liftover chain file?

Would you recommend another strategy to compare piRNA clusters across mouse strains?

I would really appreciate your insight or any suggestions on how to move forward.

Best regards,

[GenoMax]

Mouse strains can be very different, especially when you are comparing a wild derived strain to a lab inbred one. GPT lists the following differences between them. So a simple liftover is likely not going to work, which is what you seem to have discovered.

| Feature                        | PWK/PhJ                               | C57BL/6 (Black 6)                          |
| ------------------------------ | ------------------------------------- | ------------------------------------------ |
| **Origin**                     | Wild-derived (Mus musculus musculus)  | Classical inbred (Mus musculus domesticus) |
| **Genomic Diversity**          | Very high                             | Low                                        |
| **Number of SNPs vs. Black 6** | \~20+ million                         | N/A (reference genome)                     |
| **Subspecies**                 | musculus                              | domesticus                                 |
| **Mitochondrial Origin**       | musculus                              | domesticus                                 |
| **Phenotypic Differences**     | Many (immunity, behavior, metabolism) | Standard reference strain                  |