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In light of #87 and recent work on cfDNA internucleosomal methylation, does it make sense to have a feature in modkit that samples a position-dependent methylation calling threshold?
If something l…
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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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hi,
my data is cfDNA data from target panel sequencing with high coverage .
so Pisces is Ok for my data to call somatic mutation with tumor only sample ？？
thank you in advance !
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We have a user who tried to copy a directory on rhino to S3.
There were two files in the directory that had owner read permissions but no group read permissions (and this user is in the group but is…
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hello
--maxFracCNASubclone=MAXFRACCNASUBCLONE
Exclude solutions with fraction of subclonal events greater than this value. Default: [0.7]
The Frac. CNA Subclonal: 0.99 of my result is …
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I am running ichorcna as a tool to analyze my cfDNA data WGS. I do have an issue. One of the further analysis I would like to perform is to run GISTIC to get a bit more information on the data, and I …
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Hello ichorCNA team! I'd like to know if your softwar can also be used to analyze shallow whole genome sequencing data comming from tumor tissue samples (not cfDNA but solid samples of the actual tumo…
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Hi, I spotted this repo and I was wondering if there is any documentation on the underlying algorithm. What's the rationale for this deduplication method to be optimized for cfDNA? Thanks in advance.
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After running this command:
/nfs/sw/bwameth/bwameth-0.2.0/bin/bwameth.py --reference methylation_cfDNA/resources/bwameth/hg19.fa trunc_test/trunc_test.R1.fastq trunc_test/trunc_test.R2.fastq --threa…
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Greetings,
Here is the command we tried on the test bam file (actually, we also tried the program on our own bam files, and get the same result).
`msisensor-ct msi -D -M ./models_hg38 -t ./test…