User: markus.riester

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Posts by markus.riester

<prev • 79 results • page 1 of 8 • next >
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Comment: C: PureCN mappingbiasfile and minimum number of NormalDB samples question
... Mutect works fine without normals. You need to do extensive filtering though. I think that’s why they don’t recommend it. ...
written 5 weeks ago by markus.riester510
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Answer: A: Not able to find barcode file for Spatial Transcriptomic data
... Seurat only supports Visium, not the older ST assay. I have a wrapper in https://github.com/lima1/sttkit that generates a Seurat object compatible with all their Spatial* functions. ...
written 5 weeks ago by markus.riester510
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Comment: C: purecn with cnvkit
... Sorry for the late response. You will also need to install the main GenomicsDB repository. Once this compiled successfully, add that path in configure.args. Follow their install instructions closely, they did a great job there. I was planning to release a docker file with those added, but might tak ...
written 8 weeks ago by markus.riester510
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Comment: C: purecn with cnvkit
... Yes, the pon.vcf.gz unfortunately does not provide detailed enough information. Ideally, install the https://github.com/nalinigans/GenomicsDB-R. There is a shell script on GitHub that installs it (from the same author). This will make PureCN be able to read the pon_db. ...
written 9 weeks ago by markus.riester510
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Answer: A: purecn with cnvkit
... Hm, it should not crash, but can you try the complete Mutect2 workflow with the latest GATK 4?https://gatk.broadinstitute.org/hc/en-us/articles/360035531132 ...
written 9 weeks ago by markus.riester510
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Comment: C: purecn with cnvkit
... You can install the latest version from GitHub. If BiocManager is not available for your R version, try devtools::install_github. PureCN 1.20.0 is the only version that works with GATK4. I would also recommend updating GATK4. ...
written 9 weeks ago by markus.riester510
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Answer: A: purecn with cnvkit
... Can you update to the latest version 1.20.0? See https://github.com/lima1/PureCN#installation ...
written 9 weeks ago by markus.riester510
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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 3 months ago by markus.riester510
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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 5 months ago by markus.riester510
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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 5 months ago by markus.riester510

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