User: jared.andrews07

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jared.andrews071.8k
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Ph.D. candidate at Washington University in St. Louis. I have a strong interest in the development of high-performance, flexible bioinformatic tools that can integrate multiple -omics datasets to yield interesting and plausible conclusions that can then be experimentally validated.

Avid Python user and fledgling developer. Strange fascination with ostriches.

Posts by jared.andrews07

<prev • 245 results • page 1 of 25 • next >
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Comment: C: Install trimmomatic on windows computer?
... The commands to the program would be the same, it just might be slightly different to install. However, if you use the Windows Subsystem for Linux, you can just follow the linux install instructions and get familiar with the best platform for general bioinformatics on a Windows machine. ...
written 3 days ago by jared.andrews071.8k
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Comment: C: TFBS enrichiment analysis
... [PWMenrich](http://bioconductor.org/packages/release/bioc/html/PWMEnrich.html) may work for you then, though I've never used it and can't vouch for its results/ease of use. ...
written 27 days ago by jared.andrews071.8k
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Comment: C: TFBS enrichiment analysis
... What do you mean their transcription factors? TFs that bind to their promoters? Regardless, [HOMER](http://homer.ucsd.edu/homer/microarray/index.html) or [AME](http://meme-suite.org/tools/ame) from the MEME suite are probably your best bets. From a quick glance, it doesn't seem like the TFBStools pa ...
written 27 days ago by jared.andrews071.8k
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Answer: A: ChIP-Seq annotation question: Should gene annotation based on the nearest TSS or
... This is a tricky question, as regulatory elements can impact genes that are several 100kb away. Higher confidence annotations really require more information, such as correlations with gene expression, chromatin interaction information, higher order genome structure (looping, TADs), and more. Most p ...
written 4 weeks ago by jared.andrews071.8k
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Comment: C: How to run Snakemake pipeline from .py file instead of .smk file.
... Yeah, then you really just need to write a file with python and use variables to change anything dynamic as needed. What specifically are you having an issue with? ...
written 4 weeks ago by jared.andrews071.8k
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Comment: C: How to run Snakemake pipeline from .py file instead of .smk file.
... I completely agree with Wouter, this seems needlessly complex and likely more difficult to maintain than a straightforward snakemake pipeline. Regardless, the [subprocess](https://docs.python.org/3/library/subprocess.html) module will let you call external commands from within python. Basically all ...
written 4 weeks ago by jared.andrews071.8k
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Comment: C: Humbly Requesting Interviews & Responses on How to Improve Bioinformatics Softwa
... This is incredibly broad. Without more specific questions, you're unlikely to get any useful feedback. At a minimum, you should change this to the "Forum" format. ...
written 4 weeks ago by jared.andrews071.8k
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Answer: A: ChIPQC BiocParallel errors
... Can't see the error, but I've also run into many of them with the ChIPQC/DiffBind family of packages related to BiocParallel. They just don't seem to handle the parallelization well (or consistently). After loading the `BiocParallel` package, try setting it to run in serial, which usually fixes the ...
written 5 weeks ago by jared.andrews071.8k
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Comment: C: How to choose good tools for identifying functional SNPs?
... Great list. Don't forget the [Variant Effect Predictor](https://useast.ensembl.org/info/docs/tools/vep/index.html) (Coding/Protein, mostly), [SnpEff](http://snpeff.sourceforge.net/) (variety of fields), and [DeepSea](http://deepsea.princeton.edu/job/analysis/create/) (Non-coding/Regulatory). ...
written 9 weeks ago by jared.andrews071.8k
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Comment: C: How can I call somatic CNV in tumor samples with no reference (control) samples?
... To add to Kevin's answer, I've also found the [Database of Genomic Variants](http://dgv.tcag.ca/dgv/app/downloads?ref=GRCh37/hg19) to have excellent sets of common germline CNVs that can help you filter out many of them. His other points still hold true - having a matched reference is best. ...
written 9 weeks ago by jared.andrews071.8k

Latest awards to jared.andrews07

Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Scholar 5 weeks ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: How to choose good tools for identifying functional SNPs?
Scholar 10 weeks ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Scholar 12 weeks ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Scholar 4 months ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Scholar 5 months ago, created an answer that has been accepted. For A: How to make variant calling run faster?
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Scholar 5 months ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Scholar 5 months ago, created an answer that has been accepted. For C: Combining vcf files so that same loci data is combined
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Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Scholar 5 months ago, created an answer that has been accepted. For A: How to make variant calling run faster?
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