User: Maarten Slagter

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Posts by Maarten Slagter

<prev • 12 results • page 1 of 2 • next >
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Answer: A: Description of alt loci in ref genome GRCh38.d1.vd1
... Through GenBank Accession GCA_000786075, I found the following report that lists all decoys as unplaced scaffolds: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/786/075/GCA_000786075.2_hs38d1/GCA_000786075.2_hs38d1_assembly_report.txt ...
written 22 days ago by Maarten Slagter80
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Description of alt loci in ref genome GRCh38.d1.vd1
... Hi all Can anyone point me to a description of GRCh38.d1.vd1 (used by the TCGA GDC) and the alternate loci in particular? Is it an adaptation of one of the 'GRCh38.p\d{1,2}' genomes? You'd think NCBI knows about all ref genomes, but this one is not included. The information provided by the TCGA ne ...
alternate loci tcga reference genome written 22 days ago by Maarten Slagter80
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Comment: C: TCGA/Broad Institute CNV Files Segment Mean
... If they are truly log2 ratios of the tumor CN to the normal CNs, how can it be that I see the following in the TCGA ACC cohort?                          sample chromosome start      end num_probes segment_mean 1: TCGA-2H-A9GF-01A-11D-A37B-01          1 61735 15024591       7600       0.0713 2: TCGA ...
written 2.8 years ago by Maarten Slagter80
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Comment: C: Variant allele frequency in TCGA and ICGC
... Thanks once again, this is very useful. I found the oncotated MAFs offered by the Broad also to be very complete they don't seem to offer complete MAFs for THYM, MESO and ESCA.  I noticed that the column names deviate from what's supposed to be there in the readme. In the STAD and SKCM files I find ...
written 2.9 years ago by Maarten Slagter80
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ICGC data ontology
... Hello everyone, TCGA provides sample preparation and sequencing information in MAGE TAB format along with the primary data (see here). Does the ICGC provide something similar? I can't seem to find anything like it on the website nor through Google. In particular, I wonder: Have variants been (r ...
mage-tab icgc sdrf written 3.0 years ago by Maarten Slagter80 • updated 2.9 years ago by Biostar ♦♦ 20
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Comment: C: Variant allele frequency in TCGA and ICGC
... Thanks a lot Cyriac! That's an impressive amount of columns you'ved added and indeed makes this data very attractive. We're striving to conduct a pan-cancer analysis and would highly prefer to restrict ourselves to donors for which RNAseq is also available - granted that this restriction will leave ...
written 3.0 years ago by Maarten Slagter80
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AND filter in ICGC data portal?
... Hi all I'm wondering whether it is possible to filter donors in ICGC's data portal based on the availability of both EXPS and SSM, right now I seem to be only be able to select donors for which either EXPS and/or SSM is available. If not through the portal, maybe this possible using the HTTP API? I ...
data portal icgc restful http written 3.0 years ago by Maarten Slagter80
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Answer: A: Variant allele frequency in TCGA and ICGC
... For future reference in this rather daunting task of finding pan-cancer MAFs, there is no standard column that stores VAF in TCGA MAFs (https://www.biostars.org/p/105870/) but rather there are varying column names between the GDACs that created the MAFs.  In addition to Sean's link, this page by th ...
written 3.0 years ago by Maarten Slagter80
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Answer: A: Where to download latest TCGA MAF files?
... This page should list all the latest MAF files https://wiki.nci.nih.gov/display/TCGA/TCGA+MAF+Files This page contains derived somatic MAF files https://confluence.broadinstitute.org/display/GDAC/MAF+Dashboard ...
written 3.0 years ago by Maarten Slagter80
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Comment: C: Variant allele frequency in TCGA and ICGC
... Thanks once again! The UCSC produced MAF files I looked at indeed include REF and ALT allele counts. Is there a 1-to-1 correspondence between presence of this field in the MAF file and presence in the corresponding protected VCF file? In other words, would it be useful to apply for access to the pro ...
written 3.0 years ago by Maarten Slagter80

Latest awards to Maarten Slagter

Teacher 11 days ago, created an answer with at least 3 up-votes. For A: Variant allele frequency in TCGA and ICGC
Appreciated 20 months ago, created a post with more than 5 votes. For Variant allele frequency in TCGA and ICGC
Great Question 20 months ago, created a question with more than 5,000 views. For Variant allele frequency in TCGA and ICGC
Popular Question 20 months ago, created a question with more than 1,000 views. For ICGC data ontology
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Variant allele frequency in TCGA and ICGC
Student 3.0 years ago, asked a question with at least 3 up-votes. For Variant allele frequency in TCGA and ICGC

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