chocotwig

Mapping transcripts to nanopore genomic reads

2

Hi, I use the following command to map transcripts to my individual nanopore genomic reads: `./minimap2-2.17_x64-linux/minimap2 -c -x map-ont -G4000 -F4000 -g4000 -r4000 --hard-mask-level -M 0 --secondary=no -uf -C5 transcriptome.fa...

Hi, I have assembled a genome using nanopore long reads. No reference is available for this genome. In addition to BUSCO, I want to assess the completeness of this assembly...

Hi, I observe that while I can manually draw out a single path between, say 5 reads, miniasm only generates a contig that has >2x read coverage at all locations...

Hi, I have a conceptual question about miniasm. Say I have several thousand genomic reads, and I know that 100 of these reads represent a given genomic region, and that...

No improvements to assembly seen

4

Hi, I used TopHat to align my RNAseq PE reads. I'm getting absolutely no improvements on the final assembly, and I'm suspicious that I'm doing something wrong, because I did...

Base-level error rate is high in assembly. Suggestions?

2

Hi, I'm trying to apply Rascaf to an assembly that is unpolished and has high base level errors. I still want to try out Rascaf, and I was wondering if...