User: bari.ballew
bari.ballew • 90
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- @BariBallew
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Posts by bari.ballew
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... It looks like you may have duplicated part of your path. Right now, your path to your data reads:
`/t6/h7/data/expression/t6/h7/data/expression/demo_data/{sample}_R1.fastq.gz`
I'm assuming you need to access the paired fastq files in tandem for alignment or something similar. Try something like t ...
written 11 days ago by
bari.ballew • 90
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... Just using bash:
```
for i in *fasta; do n="${i%.fasta}"; sed -i.bak "s/>[^_]\+/>$n/" $i; done
```
This loops over all files in the current directory that end with "fasta". For each file:
1. `n="${i%.fasta}"` removes the .fasta file extension (can be generalized to any extension by using ` ...
written 27 days ago by
bari.ballew • 90
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... Hi Sean! Did your group ever explore options for this sort of QC? We are currently using VerifyBamID for both germline and tumor/normal data, but we are concerned with the possibility that it will erroneously interpret somatic copy number changes in tumor samples as contamination. Thinking about ...
written 27 days ago by
bari.ballew • 90
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Comment:
C: MAF file having mutation data
... Yes, any potentially identifiable data in GDC falls under controlled access. From GDC's documentation:
> Open access data generally includes high level genomic data that is
> not individually identifiable, as well as most clinical and all
> biospecimen data elements.
>
> Controlle ...
written 9 weeks ago by
bari.ballew • 90
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Comment:
C: MAF file having mutation data
... A MAF file is just a list of mutations found in a given sample(s). You can find mutations in either WES or WGS data, so you can have a MAF file (or a VCF file) for either type of experiment. For WGS, you are looking at mutations across the whole genome, so you will likely have more mutations liste ...
written 9 weeks ago by
bari.ballew • 90
0
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Answer:
A: MAF file having mutation data
... TCGA has both WES and WGS data. If you're looking at WES data, you'll see mainly protein-coding mutations, as this is what exome sequencing focuses on. If you're looking for non-coding regions, you may be more interested in the whole genome data. ...
written 9 weeks ago by
bari.ballew • 90
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... Just realized this is an older question, but I already wrote up an answer so hopefully this is still helpful!
First, regarding merging somatic, germline, and LOH files for SNPs and indels: this depends on the question you're trying to answer, but you probably don't want to merge them, at least at f ...
written 10 weeks ago by
bari.ballew • 90
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... There are several major algorithms that are used to find large deletions (structural variants, or SVs). Most of them rely on a pair of sequencing reads spanning the breakpoints of the SV. If you have WGS data, the chance that you sequenced across the breakpoint is pretty good, but for WES data, it ...
written 10 weeks ago by
bari.ballew • 90
1
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1
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... You probably want to check out Broad's best practices (https://software.broadinstitute.org/gatk/best-practices/). Specifically, look mainly at the sections on data pre-processing and germline SNPS+indels. Alternatively, you could check out the bcbio pipeline (http://bcbio-nextgen.readthedocs.io/en ...
written 16 months ago by
bari.ballew • 90
Latest awards to bari.ballew
Scholar
9 weeks ago,
created an answer that has been accepted.
For A: tool to detect large deletions
Teacher
9 weeks ago,
created an answer with at least 3 up-votes.
For A: tool to detect large deletions
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