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as of the merge of #160, charcoal now performs the following steps -
1. find candidate genomes for contamination analysis, based on sourmash shared hashes with GTDB r95
2. download genomes and per…
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https://github.com/gatk-workflows/five-dollar-genome-analysis-pipeline/blob/70025d47d2aea47043effa63f4f5d619004c9c7c/tasks/Qc.wdl#L319
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Hi developer,
I just want to make sure I am on the right track to make my own index. Because repbase is not openable, I downloaded the fasta file from GENCODE (Genome sequence, primary assembly (GR…
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Dear @fasnicar
Thanks for this amazing tool! I have already run it once and it went smoothly and the results were very informative.
However, I am trying to run the analysis again but I am a bi…
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the taxonomic analysis in #35 and the protein comparisons in #40 as well as the sample summaries in #42 can all be usefully done immediately after the gather and genome information is calculated.
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Dear Nadia,
i would like to ask you one more question considering what i want to achieve in my analysis using your software.
i do not have a very decent genome annotation, but i want to use the …
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Hello, I am trying to split my 10X output to one bam file per cell for some downstream analysis.
I guess one way to do it is by listing every cell barcode in a tsv file and run:
`subset-bam -b /u…
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Draft copy in:
https://github.com/edsu7/nf-core-argogermline
payload branch:
https://github.com/icgc-argo-workflows/argo-modules/tree/germline_variant_payload
Once testing is done can be forked …
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Hi,I am using the scATAC seq data from your article 'Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19'. The effect of using Signac software for …
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Hi!
I'm trying to run STAR-Fusion with the coding effect option. Here is the command that I ran:
```
cd /fs/ess/PAS0854/Emily/kinase_fusions/head_neck/other_datasets/sartor_2022/SRR2932813/
…