User: markus.riester

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Posts by markus.riester

<prev • 72 results • page 1 of 8 • next >
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Answer: A: TCGA capture kits
... Yep, GDC provides that information. See here for a script to download it:https://github.com/lima1/PureCN/issues/137 ...
written 4 weeks ago by markus.riester500
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Comment: C: PureCN prepare environment error
... See section 2 of https://bioconductor.org/packages/release/bioc/vignettes/PureCN/inst/doc/Quick.html for links to precomputed map-ability files. Rep timing should be available from UCSC genome browser. It’s not critical and safe to run without. ...
written 11 weeks ago by markus.riester500
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Answer: A: PureCN mappingbiasfile and minimum number of NormalDB samples question
... 4 normals should work for coverage normalization and is certainly better than nothing for mapping bias estimation. I usually recommend 10 normals from ideally 2-3 different batches, but got good results with less than that. For mapping bias, 7 is the minimum number to fit beta binomial distribution ...
written 12 weeks ago by markus.riester500
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Comment: A: TCGA CNV data reformatting
... Yes, you can safely add them. In short segments you sometimes have not enough heterozygous SNPs to resolve major and minor, but total should be still reliable. I guess that’s the reason there is a separate column for total in your template. ...
written 3 months ago by markus.riester500
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Answer: A: TCGA CNV data reformatting
... You will need the ABSOLUTE or ASCAT output. There are TCGA pan cancer papers providing the former for at least most of the datasets. ABSOLUTE will get you the missing columns 6 to 10. ...
written 3 months ago by markus.riester500
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Comment: C: PureCN Coverage.R error
... Weird. That’s a new one. Can you share the input BED file? Via github issue or email. But removing the overlaps as mentioned in the warning should fix it. It should do it automatically, but I guess some intervals are repeated multiple times and merged only once. ...
written 3 months ago by markus.riester500
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Comment: C: PureCN Coverage.R error
... Looks like there are still some issues with the interval files. Can you share the command line and output of both IntervalFile.R and Coverage.R? ...
written 3 months ago by markus.riester500
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Answer: A: PureCN prepare environment error
... Thanks. If you think this is something that should have been handled with a better error message, feel free to open a github issue with a minimal example to reproduce. ...
written 3 months ago by markus.riester500
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Comment: C: PureCN prepare environment error
... Hm, this shouldn't be that difficult. Did you run samtools faidx GRCh38.d1.vd1.fa? This should probably warn you when something is wrong with the Fasta. ...
written 3 months ago by markus.riester500
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Comment: C: PureCN prepare environment error
... Glad you figured it out. Bioconductor should be able to work with uncompressed Fasta files if they are sorted (the official genome build Fasta files are). See the underlying ?scanFa function. ...
written 3 months ago by markus.riester500

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