User: bjwiley23
bjwiley23 • 20
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- 1 year, 1 month ago
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Posts by bjwiley23
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... 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
bjwiley23 • 20
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... 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
bjwiley23 • 20
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... Anbody know why most POPAF=7.3? ...
written 5 weeks ago by
bjwiley23 • 20
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... Can you do this for boxplots also? ...
written 5 weeks ago by
bjwiley23 • 20
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... 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 ...
written 5 weeks ago by
bjwiley23 • 20
• updated
4 weeks ago by
Kevin Blighe ♦ 71k
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... 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
bjwiley23 • 20
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... 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
bjwiley23 • 20
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... 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
bjwiley23 • 20
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... 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
bjwiley23 • 20
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... 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
bjwiley23 • 20
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