User: bjwiley23

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bjwiley2320
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1 year, 1 month ago
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Posts by bjwiley23

<prev • 29 results • page 1 of 3 • next >
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Comment: C: What is the right illumina universal adapter sequence for trimming paired-end re
... I tried running flexbar with the longer adapters and it didn't remove any of the adapters. fastqc shows same. ...
written 14 days ago by bjwiley2320
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Comment: C: How accurate is the IBD calculation by plink?
... Where is good place to start to understand this relationship? It seems like plink documentation would rather give 5 hints than 1 explanation. ...
written 28 days ago by bjwiley2320
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Comment: C: issue in the vcf format using Mutect2
... Anbody know why most POPAF=7.3? ...
written 5 weeks ago by bjwiley2320
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Comment: C: Adding asterisks to a ggplot2 bar plot to show significance
... Can you do this for boxplots also? ...
written 5 weeks ago by bjwiley2320
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APT rma-sketch gene has same values as exon - Affymetrix Human Exon 1.0 ST Array
... Hi, I have below code to summarize the exon and gene intensities. I am wondering why for 1 gene it has the same values (logged) as one of the probes so that when doing Gene-level Normalized intensity subtracting (since its logged) I'll get 0 for each sample. How is this the case that gene level in ...
exon-array apt written 5 weeks ago by bjwiley2320 • updated 4 weeks ago by Kevin Blighe71k
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Comment: C: GATK DepthOfCoverage: 'total coverage' and 'mean coverage' meaning
... What output format is your -genelist for refseq. I tried bed, gtf and all fields from UCSC and none have worked for me. Can you attach this list? ...
written 5 weeks ago by bjwiley2320
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Comment: C: Might @PG headers affect downstream analyses, and how can I safely remove them f
... Do not all of Picard tools add @PG lines? I ran AddOrReplaceReadGroups and there was no @PG line for this but running MarkDuplicates there was. ...
written 6 weeks ago by bjwiley2320
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Comment: C: Difference between exon positions in hg19 and b37?
... just for anybody who lands here first. [This](https://www.biostars.org/p/299110/) is updated answer using bcftools. still need Devon's file(s). ...
written 6 weeks ago by bjwiley2320
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Comment: C: Filtering on the minor allele in VCFtools
... GATK indicates they do this for their [best practices](https://gatk.broadinstitute.org/hc/en-us/articles/360035890631-Panel-of-Normals-PON-) and then makes the reader scavenger around the internet to find how to do this instead of giving a resource. Shame. ...
written 6 weeks ago by bjwiley2320
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Comment: C: I got a problem with making normal reference using cnvkit
... In the `batch` command does `autobin` only run on median file of tumor samples or median file of all tumor and normal samples? ...
written 6 weeks ago by bjwiley2320

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Supporter 5 months ago, voted at least 25 times.

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