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Hello! I am attempting to patch a scaffold-assembled reference genome of a congener of my focal bird species (TANG, in the code below) with a chromosome-level reference genome of a more distantly rela…
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Develop a minimap2 alignment [see [docs](https://lh3.github.io/minimap2/minimap2.html)] function that uses minimap2 (installed via conda or in the PATH), we can run this so it produces a BAM file. The…
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Hello!
I have been using TOGA lately for transferring hg38 gene annotations to a newly constructed genome and it looks good so far! However, I do notice that annotations for non-coding RNAs such as…
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**Snakemake version**
6.10.0
**Describe the bug**
Benchmark returns wrong values whenever a tool is executed in a docker container. As seen in the example below, it took
Freebayes 1.5 hour to fi…
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### Description of the bug
Good evening,
I am experiencing problems with Sarek's pipeline. When I try to remove the adapters from my WES data, the dragmap tool runs into "Segmentation Fault".
Do y…
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when I run this:
singularity exec $pggb_path/pggb_latest.sif wfmash -t 20 $genome_path/ganganF73.genome.fa.gz --query-file-list=/home/user/huyang/shuai/data/pan_test/genome/genome.txt > aln.paf
I …
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Hi! I have used the star fusion. But have used it after star aligner. For star alignment we have used ensembl version of human genome Hg38. And for star fusion the ctat genome library files was downlo…
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### Description of the bug
I have previously processed the GRCh38 genome with bwameth for a different pipeline that I'm trying to compare with the nf-core. So I provide the following with the input c…
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Hi Jeff,
First of all, thank you for this amazing software!
I am trying to use your code for an assignment for university where I need to code a RNA to DNA mapper. I get a FASTQ file containing …
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thanks a lot, amazing work! are you planning to make it work for HUman genome as well?
regards