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Hi! I recently encountered a problem when running HiTE. After generating the genome.rename.fa.defalse file, there is no subsequent output. I tried several chromosome-level genomes of about 600Mb, usin…
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Can I use NCBI to construct a reference genome?
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Hey,
I tried the script on my data set (which is a fragmented bacterial genome extracted from a metagenome).
```bash
Rscript --vanilla plot_BAM_density.R -f ../GCA_012799365.1_ASM1279936v1_ge…
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Dear Community,
I would like to ask about the suggested coverage for the tetraploid genome.
(The targeted species is the plant. I know the suggested coverage is probably also related to heterozygo…
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Add nf-core module for `lai` to genome only mode sub workflow
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Hello - I am relatively new to bioinformatics in general, so apologies if this is simply me missing something.
I had previously run the rf-index command with no issue, which is why getting this er…
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Cross-posting from https://www.reddit.com/r/bioinformatics/comments/1g6zfu6/simpleaf_index_long_runtime/
Is there some guidance about the expected runtime of `simpleaf index` anywhere?
The post …
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### Description of the bug
This issue reports limitations in the SAMURAI pipeline's compatibility with genome builds other than hg38 and hg19. While the pipeline is functional for these two builds, s…
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### Description of the bug
Dear sarek developers,
First of all, congrats and thanks for your work.
I am new to the Nextflow/nf-core field and I am trying to run the pipeline with my own MOUSE datas…
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**Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.6.1/docs/FAQ.md**:
**Describe the issue:**
I am trying to add the flags --parse_sam_aux_fields=true --use_original_quality…