Michael Hiller

Sure, I attach the read and the genomic context around that gene. Running this reduced example gives the same alignment. [read.fa.gz](https://github.com/lh3/minimap2/files/11140434/read.fa.gz) [genome.fa.gz](https://github.com/lh3/minimap2/files/11140439/genome.fa.gz)

Alright, thanks a lot for looking into this. Conceptually, HiSat2 (and other mappers?) make a list of downstream exon candidate positions that are inferred from mappings of other reads (in...

Dear Heng @lh3 and developers, we think this is really a HiFiasm bug that may have gone unnoticed, because people always expect the second haplotype is less complete as it...

Hi, can you pls check why this scaffold different sizes in the 2bit and chain (twobit: 71766; size in chain: 71276). Was a different 2bit used for the chain alignments?...

Hmm, 100 GB should be enough. Do all jobs error or only particular ones with very big genes (I think TTN needs more mem). The other thing that could be...

interesting. Typically, such issues affect many scaffolds and thus many genes. But from what you describe, it seems like only a few small scaffolds are affected. There must be a...

Hi, sorry to hear that the lastz pipe is not working. I asked @kirilenkobm to have a look, as I don't know this code too well. --> Something I always...

Hi Vinita, thanks for posting these results. Overall I would say that hal-chains also seem to work, especially because a hal alignment can be used for several different reference species....

Hi Vinita, sorry for the slow response. TOGA keeps the gene and transcript IDs of the reference in query_annotation, as it is homology based. This tells you which genes TOGA...

@kirilenkobm Can you pls look into this? What I don't understand is what Java has to do with any of this, as TOGA doesn't use Java??