Yossi Farjoun
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Activity overview
Latest activity by Yossi Farjoun-
Yossi Farjoun commented,
Hello Pubudu, Thanks for writing in. Methods for detecting different conditions would depend on the conditions and type of data. I can conceive of a way to do this for RNA by clustering the coverag...
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Yossi Farjoun commented,
Hello Beatriz Moleirinho, Thanks for reaching out. in the paper listed above we used fingerprinting on DNAse, CHiP-Seq and RNA-seq, but not ATAC-seq. I don't see a reason why it shouldn't work as ...
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Yossi Farjoun commented,
We finally got the thumbs-up to publish the actual snp list that we use for fingerprinting....you can find it here. Also, in case you were wondering what system we are using for assaying the samp...
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Yossi Farjoun commented,
Those are really high LOD scores! I'm guessing that you're using the large HaplotypeDatabase....or that you have really really deep coverage.... Anyhow, my interpretatino of the results are that ...
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Yossi Farjoun commented,
I think I understand the question...I'll try my hand at answering. When a high-purity (I think that this is where the "impure" issue is stemming from, see note in the end) tumor sample undergoes L...
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Yossi Farjoun commented,
I realize that this is a documentation issue and will work to fix this in the spec. RGID should indeed be unique, but only within in each file. Since the IBCTS program emits multiple files, they ...
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Yossi Farjoun commented,
The documentation needs updating...you cannot specify the Readgroup ID in the LIBRARY_PARAMS file. you can specify (one) Readgroup ID via the ` READ_GROUP_ID parameter, but it will be the same id ...
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Yossi Farjoun commented,
We finally got approval to make public the full "haplotype database" that we use in production. These are designed for human samples: gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_ass...
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Yossi Farjoun commented,
Hi NawarDalila, The adapters you list seem to be very short, and they seem to only have the illumina-adapter part of the oligo rather than including the entire adapter with the sample-barcode an...
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Yossi Farjoun created an article,
Detecting sample swaps with Picard tools
By Yossi Farjoun, Associate Director of computational research methods in the Data Sciences Platform **A note to explain the context of the paper by Nauman Javed, Y.T. and others, “Detecting sample...