User: ngsgene

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ngsgene350
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Posts by ngsgene

<prev • 43 results • page 1 of 5 • next >
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Impute2 Custom Reference Panel
... Have used Impute2 for imputation with the provided reference panels (mostly 1k) and that has always worked well. For a certain project, am considering the feasibility of using a "custom" reference panel for a set of samples (~200) that are from a population, which went through a severe bottleneck. ...
impute2 imputation reference recombination map written 2.5 years ago by ngsgene350 • updated 5 months ago by Kevin Blighe19k
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Comment: C: eQTL analysis: Genotyping data, microarray expression data
... You need to click "add reply" to post a response to the comments above, instead of commenting to the main post.     ...
written 2.9 years ago by ngsgene350
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Comment: C: eQTL analysis: Genotyping data, microarray expression data
... Wrote a script to parse the plink output, MatrixEQTL needed the genotype coded as either 0,1,2 - using both alleles that you get in the plink file you can account for ref ref/ref alt/alt alt and generate the genotype input file. ...
written 2.9 years ago by ngsgene350
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Answer: A: Remove Illumina TruSeq Index adapters
... If I am correct there's something about Scythe and 5'- end, you may want to check out their readme. This post explains the thumb rule of trimming adaptors https://www.biostars.org/p/83146/  worth a look. ...
written 3.4 years ago by ngsgene350
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Answer: A: Genotype quality scores in 1000 Genomes vcf files
... What are your criteria for good calling quality? One option could be to check out their vcf files or generate PLINK files using genotype data and then generating summary statistics. Have included some links: https://www.biostars.org/p/17195/ http://www.1000genomes.org/node/101 http://pngu.mgh.har ...
written 3.4 years ago by ngsgene350
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Answer: A: IGV browser error
... Looked at their code that is throwing this error (search for the error message) seems the index file (fai) is giving issues for the fasta file you are using as a reference  //We loop through, generating a new FastaSequenceIndexEntry //every time we see a new header line, or when the file e ...
written 3.4 years ago by ngsgene350
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Answer: A: Mitochondrial D loop region
... There would be difference in the various builds out there, this link puts some light on that: http://haplogrep.uibk.ac.at/blog/rcrs-vs-rsrs-vs-hg19/ If you're using rCRS MITO MAP offers the fasta file and coordinate info, similarly NCBI should have others too. D-loop complement(join(160 ...
written 3.4 years ago by ngsgene350
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Answer: A: mitochondrial variant calling
... Depends on what you are primarily looking to do, for the clinical panel we used rCRS as the reference sequence and aligned MT reads - there weren't autosomal chromosomes sequenced to begin with but I would suggest you look into Varscan along with GATK (unless thats the only tool supported by your pi ...
written 3.4 years ago by ngsgene350
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eQTL analysis: Genotyping data, microarray expression data
... After referring to some posts on Biostars am leaning towards using Matrix eQTL for eQTL analysis using genotyping data (plink format) and microarray expression data (either analyzed through Partek or R packages)  Am looking for some blog posts / user experiences of having done something similar, I ...
matrix eqtl R partek plink eqtl written 3.4 years ago by ngsgene350 • updated 2.9 years ago by Zhenyu190
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Comment: C: Error when loading file into PLINK
... Thanks Maxime, got that figured out. ...
written 3.4 years ago by ngsgene350

Latest awards to ngsgene

Epic Question 3.3 years ago, created a question with more than 10,000 views. For How To Find Paralogs Using Blast
Appreciated 3.4 years ago, created a post with more than 5 votes. For A: From Single Line To Fasta Format ?
Scholar 3.4 years ago, created an answer that has been accepted. For A: Mitochondrial D loop region
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: From Single Line To Fasta Format ?
Appreciated 5.6 years ago, created a post with more than 5 votes. For A: From Single Line To Fasta Format ?
Great Question 5.6 years ago, created a question with more than 5,000 views. For How To Find Paralogs Using Blast
Popular Question 5.6 years ago, created a question with more than 1,000 views. For How To Find Paralogs Using Blast
Popular Question 5.6 years ago, created a question with more than 1,000 views. For Detecting Polymorphic Sites In Multiple Sequence Aligned Files
Supporter 5.6 years ago, voted at least 25 times.
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: From Single Line To Fasta Format ?
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: Searching For A Simple Yet Powerful Workflow For Rna-Seq
Student 5.6 years ago, asked a question with at least 3 up-votes. For Detecting Polymorphic Sites In Multiple Sequence Aligned Files

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