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I have used the following options :
subcommand:
- segment --drop-low-coverage --drop-outliers
- call -filer ci ,sem ,ampdel,cn
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I don't know if the author is aware of the issue with incomplete removal of sequence adaptors and barcodes.
Specifically, when using tools such as Dorado Demux, Porechop, and Guppy_barcoder to trim a…
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Hi
I am trying to use FirstSV for prostate cancer cfdna data and I have encountered some errors while running.
I have downloaded the simple repeats file from UCSC GoldenPath and I get the followi…
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I am using `fgbio Version: 0.9.0-0dda145-SNAPSHOT` to run `GroupReadsByUmi` on a sorted, mapped BAM with duplex RX tags and am running into the following error:
```
...
[2019/09/10 15:04:29 | Gr…
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I have the following error messages from running the command "pip install -r requirements.txt'.
D:\cfdna-main\cfdna-main>pip install -r requirements.txt
WARNING: Ignoring invalid distribution -ip …
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Hi Nanopore team,
I noticed a significant (~10x) slow down of the Dorado basecaller when adding the 6mA modification model. This is notable since adding the 5mCG_5hmCG modification model have almos…
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Hi
Could you please guide me on obtaining the fixed bin set? It's a critical component for validating the GEMINI model on an independent cohort. However, I couldn't find this vital information in eit…
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I've run into an error when attempting to run the Nextflow pipeline, so thought I'd reach out in case it's something you've encountered and can quickly identify what might be causing it. Some of the o…
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(Posting here because the forked repo doesn't have issues: @gavinha, you might want to enable them)
A couple of papers suggested that selecting DNA fragments that match nucleosome size, or slightly…
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Hi Christa,
Thank you for developing CelFiE. I am trying to run CelFiE on 2 samples (adult normal lung tissues-WGBS). After getting the coverage file from Bismark, I ran your prepare_bismark.sh scr…