mappability maps for long-reads vs short-reads

[PatS]

Hi everyone,

I'd like to ask if the mappability map Homo_sapiens.GRCh38.dna.primary_assembly.fa.r101.s501.blacklist.gz can be used for long-read data when performing Delly CNV?

I've noticed that for the T2T-CHM13 assembly, there are two different mappability maps available:

• T2T-CHM13v1.1.fa.r101.s501.gz
• T2T-CHM13v1.1.fa.r501.s2001.gz

The first one is for short reads, and the second one is for long reads, correct? If so, why is there no similar map available for hg38 for long reads?

Thanks a lot!

Best regards,

Patricie

[Tobias Rausch]

Dear Patricie,

So far I am using the *.r101.s501.* maps by default. I am indeed experimenting with mappability maps better suited for long reads and regions of the genome that are difficult to map but that's still work-in-progress. I hope to have time in February to look at this in more detail.

Best, Tobias

--
You received this message because you are subscribed to the Google Groups "delly-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to delly-users...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/delly-users/0b31ac5e-35de-4b11-9481-41f091189572n%40googlegroups.com.