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After I used minimap2 to align the Nanopore third-generation sequencing data, when I tried to convert the alignment result string kstring_t to bam1_t, I used the sam_parse1 function, but it resulted i…
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Good morning,
I am currently using Freebayes ( v1.3.6) to identify variants from Oxford Nanopore sequencing data. However, I have noticed that not all the expected SNPs and insertions are being det…
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There are some issues with this training that I collect here to fix step-by-step.
* In the preprocessing part, all fastq outputs go into multiQC, but since multiQC only shows one output for identical…
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There are 14 metatranscriptome projects associated with Gs0149396. This is lower priority for GSP than processing the metagenomes b/c there are more of them.
Depends on [Add missing file_name_pattern…
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Hello, Dr. He. Sorry to bother you again.
I already knew that SEVtras would work with single cell RNA sequencing data produced by the 10x genomics chromium , which is based on droplet sequencing, but…
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Adding a new stage and jobs for a pipeline to be used by the rare-disease team.
The stage will create CRAM files from BAMs, not by re-aligning the BAMs, but by converting them.
### How this stag…
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I used sequencing data to align with Bowtie2 to the GTDB database, and then I used the gtdb_to_taxdump.py and acc2gtdb_tax.py scripts to generate name, nodes, and acc2tax files. However, I encountered…
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This is regarding the quote obtained for WGBS sequencing (#1732) .
For this sequencing run we plan to include DNA from a few different Pacific cod tissue types (blood, fin, jawbone). The blood and…
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Draft copy in:
https://github.com/icgc-argo-workflows/dnaaln
Testing commands:
1. Full pipeline work through if sequencing files and payload are local
```
nextflow run main.nf -profile debug_…
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Thank you for developing this tool; I think it might be very useful for sharing our research data.
I want to ask you for advice in applying `bamboozle` to bisulfite converted data.
Bisulfite trea…