Glennis created a hybrid t2t:

Hi David,

While looking at the CHM1 defensin locus more closely yesterday, I realized that it is NOT inverted from CHM13 but is, rather, the same orientation as CHM13 (both of which are inverted relative to hg38--I think that is what caused my confusion). Therefore, the fosmid alignments you are currently generating will not be that useful for us, since they will be very similar to your alignments to CHM13.

To address this issue, I have now made a hybrid assembly consisting of the CHM13 v1.0 genome with the chr8 defensin locus (chr8:6300000-13300000) replaced with the HG00733 H1 defensin locus. I have confirmed that this new chr8 defensin locus is inverted relative to CHM13 v1.0.

The assembly is here:
/net/eichler/vol27/projects/AlphaSatelliteMapping/nobackups/FindingAlphaSat/t2t_chr8/hg00733_chr8/defensin/chm13_hg00733_hybrid/chm13_hg00733_hybrid.fa


I'm not sure if you will see this before Monday, but if you do, can you please stop your CHM1 alignments and replace the genome with the one above and launch ABC10 and then ABC8 alignments?

Thanks, and I hope you had a great Thanksgiving!
Glennis


the chr8 you made.  did you start with the normal chm13 chr8 and invert part of it?  Or was it the chm1 chr8 that you started with?

Glennis Logsdon  2:52 PM
95% of it is chm13 chr8
2:52
5% is chm1, which is a inverted relative to chm13

the clone end mapping pipeline was done here:
/net/eichler/vol27/projects/AlphaSatelliteMapping/nobackups/FindingAlphaSat/dgordon/clone_end_mappi\
ng_ABC10_vs_hybrid4/bed