Robert Vaser
Robert Vaser
Hi Aine, were you using --no-trim parameter on branch `feature_no_trim` or not? I am asking because I also removed trimming of first/last window regardless of parameter --no-trim. Best regards, Robert
Available in version `1.4.6` at https://github.com/lbcb-sci/racon.
@johnomics & @cgjosephlee, could you also try mapping with option `-f 0` so that minimap2 does not filter out repetitive k-mers? I think that should increase coverage at telomeres.
Thanks @cgjosephlee for the evaluation! I am not sure why they are completely trimmed after few rounds. Do you perhaps know their size through iterations?
Hello, you have to run racon on sample data either with: ```bash racon -u --threads 48 sample_reads.fastq sample_overlaps.paf sample_layout.fasta ``` or ```bash racon -u --threads 48 -f sample_reads.fastq sample_ava_overlaps.paf sample_reads.fastq...
Hi Michal, as I can see you are using reads in FASTQ format? If you created them with artificial qualities, you can avoid this step and pass them in FASTA...
You can as well add an Illumina polishing step (if you have the data). Use minimap2 with `-x sr` option and racon with default arguments.
Use the wrapper when your data won't fit into memory. The interface is the same plus two new options: `--split` and `--subsample` (check the usage). Edits to script: pass the...
Hello Jon, I am afraid I did not understand your inquiry. Could you please elaborate? An example would be great. Sorry for the late response and best regards, Robert
Hello, can you please paste the whole racon log? Best regards, Robert