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Hi there,
I would like to run RepeatHMM Scan across whole genome, I suppose I need to create a file like "hg38.predefined.pa"? If so, can you share yours used in your 2020 paper?
Thanks.
Geo…
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A recombinant origin for the following three sequences was discussed here: https://virological.org/t/recombinant-sars-cov-2-genomes-involving-lineage-b-1-1-7-in-the-uk/658
```
Wales/ALDP-11CF93B/2…
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Hi,
I'm running diamond on AWS EC2, using NCBI's NR as a reference database.
But when i start to run blastx, it usually takes hundreds to thousands of seconds to Loading reference sequences... aga…
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Hi there,
I can now successfully run the grogram now. But I got a really high value in the alpha estimation (over 0.99). I believe there's something wrong with my unfolded SFS.
My SFS file goes…
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What version of BWA does MIPgen depend on?
My script is below:
```
module load bwa/intel/0.5.9
module load samtools/intel/1.2
project_name="./mips/first_try"
bwa_genome_index="path/to/Genome.…
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(EDTA) sajjad@sajjad-ThinkStation-P910:~/Downloads/EDTA$ perl EDTA.pl --genome BCMY01.fasta --species others --step all --sensitive 1 --evaluate 1 --anno 1 --force 1 -t 12
########################…
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varlociraptor 2.3.0
command
```shell
$ varlociraptor preprocess variants tmp.fasta --bam tmp.normal.sam --candidates tmp.vcf
Error: unable to open SAM/BAM/CRAM file at tmp.normal.sam
$ file tmp…
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Hi Jon,
I am using funannotate for my second genome now!
When I use the current version to do the annotate step, it complains `Annotation database data/eggnog.db not present. Use download_eggnog…
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from @gbggrant
> I've run the 167 Burkina Faso samples through the phasing pipeline. I haven't yet integrated your cohort_vcf_to_zarr script, but the VCFs for 2R and 3R are at:
> gs://malariagen/…
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Dear scruff team,
I have been trying to implement your tool for my analysis of a 10X library. I have been using the option to parallelize the demultiplexing. However, I ran into the problem that…