Robert Vaser
Robert Vaser
Hi, you misplaced the arguments in the Racon commands Please try the following: ```bash minimap2 -a B.fa A.fa > out.sam racon A.fa out.sam B.fa > out.racon.fa ``` Best regards, Robert
A = reads B = reference You can run `racon --help` to see the arguments (also `minimap2 --help`).
You can use option `-u` (`--include-unpolished`) in Racon to get all contigs back.
Hello, larger log files indicate that you are using an older Racon version. Please use the latest from bioconda (1.4.20). Best regards, Robert
Hi Terrance, quite interesting. Can you please run again with parameter `--no-trimming`? You will need to use the latest Racon version from [https://github.com/lbcb-sci/racon](https://github.com/lbcb-sci/racon). I would appreciate if you could share...
I suspect that 25x data is somehow badly distributed across the genome or something else is wrong. You can still send me the data, if it is not a problem...
I inspected a little bit what is happening with the underlying POA graphs. The breaks usually occur on windows that (I suspect) overlap repetitive regions in which a percentage of...
The average read length of your downsampled read set is 1260bp, which is quite small for ONT data (65% of reads is shorter than 500bp, while 83% of reads is...
Hello, Racon will only polish the sequences you pass into it, it will not create additional sequences. Best regards, Robert
Hi Kosuke, I am also unable to compile with `7.3.0`, neither with `9.3.0`. `7.5.0` works, so try installing it (I am not able to find it in anaconda though). Best...