User: JacobS

gravatar for JacobS
JacobS880
Reputation:
880
Status:
Trusted
Location:
Cleveland, Ohio
Last seen:
2 months, 2 weeks ago
Joined:
5 years, 2 months ago
Email:
s*******@gmail.com

Interested in precision medicine, translational bioinformatics, oncology.

Posts by JacobS

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What are the industry-leading methods of benchmarking metagenomics taxonomy identification?
... I am working on a metagenomics pipeline, and would like to compare my taxonomical predictions to a known (simulated) control along with the results from various other metagenomics pipelines. I enjoyed reading the CAMI comparative metagenomics paper and profiling of various methods and projects regar ...
metagenomics taxonomy written 12 weeks ago by JacobS880 • updated 6 weeks ago by Biostar ♦♦ 20
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What is the expected rate of SNPs within a human exome sequencing with HiSeq?
... I am sequencing human exome data and looking for clinically relevant SNPs. I am using the standard GATK workflow, applying a hard filter, and then evaluating with snpeff and looking for ClinVar SNPs. Overall, I'm getting about 1 in 25,000 exome bases being reported as a SNP at the end of GATK. Addi ...
exome snp highseq written 2.3 years ago by JacobS880 • updated 6 months ago by predeus590
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Nextseq 500 sample exome data
... I'm looking for some Nextseq 500 sample exome data. I've worked with numerous other sequencing technologies, and want to see how some of my pipelines hold up with real-world data fro this new platform.   Does anyone know of any data freely available that reflects a full human exome sequencing run? ...
exome nextseq written 2.5 years ago by JacobS880 • updated 2.1 years ago by balaszone0
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Are there any software packages available to calculate ploidy from RNA-Seq data?
... I realize copy number variation from RNA-Seq data is a poor idea since expression differences between samples will confound copy number data, but what about general inferences of ploidy? I have large RNA-Seq sets for >50 samples, and want to determine which are aneuploidy and which are not. Does ...
ploidy rna-seq cnv written 3.0 years ago by JacobS880 • updated 3.0 years ago by QVINTVS_FABIVS_MAXIMVS2.1k
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Correcting batch effects between RPKM datasets?
... I have two datasets, one with ~250 sample, and another with 7 samples. Both datasets are of RPKM values computed from human RNA-Seq. I don't have access to the primary reads files. Is there a good way to batch-correct these datasets so that I can combine them and scan for expression signatures? I'm ...
rpkm batch rna-seq dge written 3.0 years ago by JacobS880 • updated 3.0 years ago by Ying W3.8k
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Comment: C: What is a microarray "signature" and how can I compare my sample to a known sign
... I appreciate the links and am now looking into using their software packages. Is this such a large task that it is difficult to do in R? I figured such an analysis wouldn't take more than a few dozen lines of code. (I'd prefer to do this from scratch myself to ensure I understand everything that is ...
written 3.0 years ago by JacobS880
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Comment: C: What is a microarray "signature" and how can I compare my sample to a known sign
... Yes, I have normal tissue controls. My difficulty isn't calculating DGE or something, but how to compare the samples to the signature and know whether they are a 'fit' statistically. ...
written 3.0 years ago by JacobS880
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Comment: C: What is a microarray "signature" and how can I compare my sample to a known sign
... I have >50 microarrays, each representing a different sample, and I want to screen all samples for the EMT signature. ...
written 3.0 years ago by JacobS880
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What is a microarray "signature" and how can I compare my sample to a known signature?
... While reading about molecular subtyping strategies for various cancers, I have come across many papers talk about specific signatures that correlate to particular disease statuses and are defined by a collection of microarray probes. For example, this paper defines an "EMT signature." My question ...
chip ngs microarray written 3.0 years ago by JacobS880
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Comment: C: How to cluster microarray samples based on euclidean distance and a complete lin
... Solved my program, I was accidentally calling as.matrix on a matrix. It works great now, thanks!  ...
written 3.0 years ago by JacobS880

Latest awards to JacobS

Autobiographer 12 weeks ago, has more than 80 characters in the information field of the user's profile.
Popular Question 3 months ago, created a question with more than 1,000 views. For Are there any software packages available to calculate ploidy from RNA-Seq data?
Epic Question 2.3 years ago, created a question with more than 10,000 views. For Sequencing Your Own Genome! How Can It Be Done? Has Anyone Here Done It?
Great Question 2.3 years ago, created a question with more than 5,000 views. For Kegg Id Vs Cog Id, And The Best Method For Large Batch Id Assignment?
Great Question 2.3 years ago, created a question with more than 5,000 views. For Sequencing Your Own Genome! How Can It Be Done? Has Anyone Here Done It?
Good Question 2.3 years ago, asked a question that was upvoted at least 5 times. For Is It Necessary To Remove Adapters In All Orientations When Preprocessing Ngs Data?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Need A Unix Script For The Galaxy Tool: Maf To Fasta (Version 1.0.1)
Good Answer 2.3 years ago, created an answer that was upvoted at least 5 times. For A: How To Batch Grab All Ko (Kegg Ontology) Terms Associated With Each Kegg Pathway
Great Question 2.3 years ago, created a question with more than 5,000 views. For Converting Gff/Gtf + Reference To Embl Or Genbank ...Any Tools Available?
Great Question 2.3 years ago, created a question with more than 5,000 views. For How Are Paired-End Read Insert Sizes Inferred For Reporting In A Sam File?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Are there any software packages available to calculate ploidy from RNA-Seq data?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Correcting batch effects between RPKM datasets?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Need Suggestions For A Greedy Algorithm For Thoroughly Assembling Very Short Reads
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Converting Gff/Gtf + Reference To Embl Or Genbank ...Any Tools Available?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Software For Determining Pathway Differential Expression For Annotated Ngs Data?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Kegg Id Vs Cog Id, And The Best Method For Large Batch Id Assignment?
Guru 2.3 years ago, received more than 100 upvotes.
Epic Question 2.3 years ago, created a question with more than 10,000 views. For Converting Gff/Gtf + Reference To Embl Or Genbank ...Any Tools Available?
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: How To Batch Grab All Ko (Kegg Ontology) Terms Associated With Each Kegg Pathway
Great Question 3.0 years ago, created a question with more than 5,000 views. For Converting Gff/Gtf + Reference To Embl Or Genbank ...Any Tools Available?

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