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Hi @colindaven @sannareddyk @B1T0 @Colorstorm @BioNij
Wochenende ran well when we inputed cfdna fastq profiles containing human reads as well with other pathogenic reads.
We were interested in…
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In addition to cfDNA, whether the ichorCNA can be used for gDNA?
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Hi, it is a good work!
I hvae done the step1-4 sucessful, but what is the *WGS.FinaleMe.mincg7.mergerd.cov.37.bw. I can't see the file from where.
"ls ***WGS.FinaleMe.mincg7.merged.cov.b37.bw** …
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Hi, it seems `numpy` does not have `float` anymore (now it's included in `base`). I had a problem running:
```
$ svviz2 --ref ~/references/GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.modifi…
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Currently, I have been using ichorCNA for cfDNA analysis in HCC. However, results of several patients showed that their tumor fraction equal to 0. Is there a theoretical threshold for ichorCNA detecti…
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Hello,
For some data sets, I occasionally met error error "unrecognized CIGAR operator" when run gemBS map.
The debug imformation is as follows:
Bisulfite Mapping...
2019-11-14 10:16:56,579 D…
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Hello,
I have used the following config file:
```
[general]
chrLenFile = /media/prodriguez/disk1/Databases/genomes/Hsapiens/hg19/seq/chromosomes/hg19.fa.fai
window = 0
ploidy = 2,3
outputDi…
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**Hello, it is great work.**
**However, I encontered error in the very first step following your tutorial.**
**The script I was using is shown below:**
java -Xmx20G -cp "target/FinaleMe-0.…
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I'm looking at the new cfDNA methylation document put out by ONT https://community.nanoporetech.com/knowledge/know-how/cfDNA-methyl-profile and it has some figures on % methylation by read position.
…
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Command executed:
bcftools annotate --header-lines /Data/data/raja/cfdna/nextflow1/bin/syn3_header.txt LCR_FILTERED > FILTERED_hd.vcf
**java -jar -Xmx4g /Data/data/raja/cfdna/nextflow1/bin/snp…