mirkocelii

Results 8 comments of mirkocelii

sameStrand=TRUE in annotatePeak not working properly

Hi @balwierz ! I guess you have already found a way in the meanwhile :D ! I had the same problem and I created two separate TxDb for "+ genes"...

Manta output merging

This would be a great tool !

germline SV calls: keep only PASS?

Hello, I'm interested in the filtering too.

Questions about L, A, S -Lines in GFA format.

@jwinternitz I think the .gfa file is reporting only the reads used to built the assembly. duplicated or completely overlapping reads are not present. I tried to draw a plot...

Questions about L, A, S -Lines in GFA format.

Me too! I was looking for that, we probably need to align the reads again on the assembly to get the detailed coverage base by base

Questions about L, A, S -Lines in GFA format.

I agree with you, detailed coverage information could be interesting for the analysis of tandem repeat regions and rDNA

Duplicated BUSCO for polyploid genome

If hap1 and hap2 are both duplicated, it must be a real tetraploid

Tetraploid assembly results Which one should I use?

I also run hifiasm with hifi reads only (no HiC, no ultra-long reads) with the polyploid parameters, but I only got hap1 and hap2, although my sample looks hexaploid/octaploid based...