User: JacobS

gravatar for JacobS
JacobS850
Reputation:
850
Status:
Trusted
Location:
West Lafayette
Website:
http://web.ics.purdue....
Last seen:
1 year, 9 months ago
Joined:
4 years, 8 months ago
Email:
s*******@gmail.com

Core bioinformatician interested in everything bioinformatics!

Posts by JacobS

<prev • 94 results • page 1 of 10 • next >
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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 21 months ago by JacobS850 • updated 17 days ago by predeus400
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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 24 months ago by JacobS850 • updated 19 months 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 2.5 years ago by JacobS850 • updated 2.5 years ago by QVINTVS_FABIVS_MAXIMVS2.0k
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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 2.5 years ago by JacobS850 • updated 2.5 years ago by Ying W3.7k
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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 2.5 years ago by JacobS850
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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 2.5 years ago by JacobS850
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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 2.5 years ago by JacobS850
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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 2.5 years ago by JacobS850
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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 2.5 years ago by JacobS850
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Comment: C: How to cluster microarray samples based on euclidean distance and a complete lin
... Thanks for the reply Gian. I've tried transposing my matrix, but for some reason the terminal dendrogram branches still do not represent samples (there are far more of them than input samples) ...
written 2.5 years ago by JacobS850

Latest awards to JacobS

Teacher 24 months 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 2.5 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?
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Popular Question 2.5 years ago, created a question with more than 1,000 views. For Are There Any Scripts That Make Images From Gff Files?
Popular Question 2.5 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 2.5 years ago, created a question with more than 1,000 views. For Sequencing Your Own Genome! How Can It Be Done? Has Anyone Here Done It?
Popular Question 2.5 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?
Student 2.5 years ago, asked a question with at least 3 up-votes. For Correcting batch effects between RPKM datasets?
Great Question 2.5 years ago, created a question with more than 5,000 views. For Converting Gff/Gtf + Reference To Embl Or Genbank ...Any Tools Available?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For How To Get Gene Ontology Ids (Go) By Using Gis?
Popular Question 3.6 years ago, created a question with more than 1,000 views. For How To Get Gene Ontology Ids (Go) By Using Gis?
Good Question 3.6 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 3.6 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?
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Is It Necessary To Remove Adapters In All Orientations When Preprocessing Ngs Data?
Popular Question 3.6 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 3.6 years ago, created a question with more than 1,000 views. For Go Term Hierarchy -- How To Find All Children Terms From A Parent Term?
Popular Question 3.6 years ago, created a question with more than 1,000 views. For How To Batch Grab All Ko (Kegg Ontology) Terms Associated With Each Kegg Pathway?
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Sequencing Your Own Genome! How Can It Be Done? Has Anyone Here Done It?
Popular Question 3.6 years ago, created a question with more than 1,000 views. For How Are Paired-End Read Insert Sizes Inferred For Reporting In A Sam File?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Sequencing Your Own Genome! How Can It Be Done? Has Anyone Here Done It?

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