-
I'm submitting a bunch of genomes to NCBI and they want genome coverage:
>The estimated base coverage across the genome, eg 12x. This can be calculated by dividing the number of bases sequenced by…
-
Hi Ben,
The "contig" mode doesn't provide "relative_abundance" option for coverage measures. Could you please explain the reasons for this setting? What are your concerns about calculating the rela…
-
hi, I am running gusher from inside the braker pipeline. For some reason the first time I ran it on a chromosome-level assembly it worked nicely, but now, running it on a scaffold-level assembly (25K …
-
Hi Developers!!
Thanks for making such a straightforward tool for simulation. I wish to simulate reads from Mitochondrial genome reference fasta but I am confused about what distribution should I c…
-
I am trying to use findZX on reads that have already been trimmed, but I keep getting an error that only happens when I skip the trimming part of the pipeline.
Is there a way around this? Or should…
-
**Tool Details**
- **Name of tool:** methylQA medip
- **Tool homepage:** http://methylqa.sourceforge.net/
- **Tool description:** a methylation sequencing data quality assessment tool. The medi…
-
Hi All,
I would like to know what is the **coverage** and **score** value in the ipdSummary gff to consider a modified base as confident.
Example:
seqname | source | feature | start | end | s…
-
Hi! Francisco
While running the `-t abundance ` I am running into a problem with the sam to bam conversation due to a duplicate header. When I checked the grep "NODE_1753_length_683_cov_1.602310" FDS…
-
I am performing roary pangenome analysis on hp genomes and I got several annotations for the same gene in the individual genomes. For instance vacA which typically has a single copy in all genomes has…
-
Hi,
I would like to calculate the genome size from the whole genome ONT nanopore reads (~8.7 GB) for a plant genome. My aim is to assemble the mitochondrial genome from ONT nanopore reads. I knew th…