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I am applying CNVkit to targeted amplicon sequencing data by following your command:
cnvkit.py batch -m amplicon -t targets.bed *.bam
Is this command using the default bin size of 200?
Some of …
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Hi, I found that for targeted amplicon sequencing data, the mutations called by Pisces 5.2.7.47 will mostly be flagged as 'SB'. Is it a property of amplicon sequencing data or primer specificity? how …
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Hi,
I had a run with primer designer with this parameters:
Strangely, in the result, the amplicon is built over the starting point of the region. Which sequence would the pipeline take in su…
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When using sff_extract (seq_crumbs 0.1.8) on SFF files that contain amplicon reads, I get the warning:
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WARNING: weird sequences in file /srv/whitlam/bio/data/pyrotags/raw/Gasket67/Gasket67.sff…
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Hello,
Thanks for this very useful package!
I just have a few questions after runnning on single-cell ATAC-Seq libraries generated from the 10X multiome kit. I ran using the following commands:
…
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Look at the global distribution of phaeo species based on Tara 18S v9 data
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Hi, Dr. Hu. I met error when I performed differential analysis by LOCOM. The following is my codes:
The amplicon_ps_genus.RDS dataset is [here](https://github.com/XbiomeAnalysis/Microbiota_notes/…
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I want to use MGcounts's ability to find communities of multimapping features, on some sequencing data of synthetic constructs. I have made a fasta, aligned to it, and made a fake gtf file with all of…
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Hi Rory,
I am simulating SARS-CoV-2 diluted in a bacterial environment. My configuration file looks as follows :
```
output_path = "$SIM_DIR/pod5_files"
target_yield = $TARGET_YIELD
pore_type =…
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### Is your feature related to a problem?
No
### Describe the solution you'd like
It is nice to have the "coverage along amplicons" graphs. However, it would be very helpful if there was a way to a…