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I ran Dorado with the command: dorado correct -m herro-v1 filter.fq > corrected.fasta 2> log
The log file shows:
[2024-08-01 20:37:12.161] [info] Running: "correct" "-m" "herro-v1" "filter.fq"
[202…
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Hello, I have a question, is possible polish the primary/alternate and haplo1/haplo2 with illumina reads?
Thanks so much.
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Hi, run command :
singularity exec -B $PWD:$PWD braker3.sif braker.pl --useexisting --species Brachymystax_lenok1 --genome ./s3_repeats_screen/A1.genome.masked.final.fasta --prot_seq ./s1_input_da…
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Hi Brant!
I am wondering if there is a way to generate a file like the joined_allele_sequences_all_samples.fasta file using the new phasing workflow in 1.7.3. I would like to get alignments of phas…
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When adding deletions, the VCF shows them as insertions.
REF and ALT are back to front?
CC: @kristyhoran
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Hello,
I've been trying to use wgd V2 to calculate a Ks peak
I've taken a subset of my CDS (~3K sequences)
When I run
```
wgd dmd subset.fasta
```
I get:
![Screenshot 2024-06-25 at…
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My circlator (Circlator version: 1.5.5) run with the following command was running for 3 days and then stopped and never continued. Here is the last part of the log file:
Command:
```
circlator a…
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# Issue Report
## Please describe the issue:
Hello, I received a segmentation fault error when running dorado correct (v0.7.3). The data I am trying to correct is duplex basecalled reads. I have…
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While running what is listed as "Step 2a" in the Running Braken guide, I get the following error:
> classify: malformed fasta file - expected header char > not found
0 sequences (0.00 Mbp) process…
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https://github.com/brouwern/compbio2021/blob/4fc22d26cd66119a177fd9572bd409ffa989216d/MSA-walkthrough-assignment-part01.Rmd#L141
I am still a bit unsure exactly what the FASTA function is "cleaning…