User: nchuang

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nchuang200
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Posts by nchuang

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Comment: C: "ERROR:...Base position exceeds Integer.MAX_VALUE" using Refined IBD with map fi
... Did you figure this out? I'm having the same error with beagle ...
written 4 weeks ago by nchuang200
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how to merge genetic map of ChrX nonPAR with PAR1 and PAR2 for imputation?
... I am trying to impute with beagle my vcf calls on chromosome X. The Beagle website provides a plink genetic map file for GRCh38 with ChrX, PAR1, PAR2. I get an error when I try to run my VCF with them. I tried manually merging them but I guess the Cm would be off? How can I merge the 3 files into on ...
imputation plink beagle written 4 weeks ago by nchuang200
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How to decide method for imputing the missing genotype in a VCF
... Trying to understand the various ways to perform imputation with the available tools published in the field. My understanding is that imputation is frequently used to help fill in missing data when working with SNP arrays. However, what do you do if you have a large variant call file from whole geno ...
shapeit impute2 imputation beagle written 5 weeks ago by nchuang200
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Possible to call variants from PacBio reads from a mixed sample?
... For whatever reason my PI decided to submit many long amplicons for PacBio sequencing without barcoding each amplicon. He now wants to know how much variation exists between the samples. I was looking at the Long Amplicon Analysis (LAA) tool and it says it can generate consensus based on unique indi ...
long reads pacbio snp written 14 months ago by nchuang200
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Comment: C: CpG Methylation data from PacBio sequencing
... Thank you this is what I was looking for. I don't know how to accept this as the answer, but perhaps it's not the direct answer to my posted question. ...
written 14 months ago by nchuang200
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Comment: C: CpG Methylation data from PacBio sequencing
... https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2879396/ > For sequencing of the subsection of the fosmid (Fig. 5 and > Supplementary Figs. 3 and 4), an ∼3.7 kb segment (corresponding to > positions 12797-16484 within the fosmid) containing 13 instances of > the GATC sequence context was P ...
written 14 months ago by nchuang200
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CpG Methylation data from PacBio sequencing
... Sorry if this is a dumb question, but I am told by our sequencing core that you cannot detect methylation status of PCR amplicons with PacBio? Is that merely because the amplicons won't retain the methylated nucleotides? I was looking at the Nature Methods paper that is cited for this method of dete ...
next-gen epigenetics pacbio sequencing written 14 months ago by nchuang200 • updated 14 months ago by Antonio R. Franco4.3k
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Comment: C: VIew reads sorted by name in IGV
... I think dariober asked me the same thing and I explained it very briefly. I am just using IGV for visualization of my alignments and "reads" are actually individual consensus sequences I have sequenced and assembled separately. I want to line them up on IGV to see base differences between the assemb ...
written 2.2 years ago by nchuang200
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Comment: C: VIew reads sorted by name in IGV
... I was trying to simplify my question. My "reads" are consensus sequences of loci of interests that I named. One I did with Sanger sequencing and the other with PacBio. ...
written 2.2 years ago by nchuang200
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Comment: C: VIew reads sorted by name in IGV
... thanks Pierre. I spent a few hours trying to figure this out at least now I know it cannot be done. I did try right clicking and sorting the alignment but it does not do it by name. ...
written 2.2 years ago by nchuang200

Latest awards to nchuang

Great Question 13 months ago, created a question with more than 5,000 views. For Best way to convert VCF to PLINK file format and merge chromosomes?
Great Question 13 months ago, created a question with more than 5,000 views. For GWAS: when is it appropriate to add covariates?
Popular Question 13 months ago, created a question with more than 1,000 views. For How to setup Vi or Vim in Cygwin?
Popular Question 13 months ago, created a question with more than 1,000 views. For How to create empty Biopython MultipleSeqAlignment object?
Popular Question 13 months ago, created a question with more than 1,000 views. For What could account for these strange SNP discrepancies?
Popular Question 13 months ago, created a question with more than 1,000 views. For General approach for genotype refinement after GATK processing?
Popular Question 13 months ago, created a question with more than 1,000 views. For Using a Multiple Seq Alignment tool for pairwise alignments possible?
Popular Question 13 months ago, created a question with more than 1,000 views. For Hardy-Weinberg assumptions in variant calling
Popular Question 13 months ago, created a question with more than 1,000 views. For Reliable alignment tool for similar sequences of similar length other than Mummer?
Popular Question 13 months ago, created a question with more than 1,000 views. For Substitution matrices to score variation between protein sequences?
Student 13 months ago, asked a question with at least 3 up-votes. For Best way to convert VCF to PLINK file format and merge chromosomes?
Popular Question 14 months ago, created a question with more than 1,000 views. For How to setup Vi or Vim in Cygwin?
Appreciated 23 months ago, created a post with more than 5 votes. For GWAS: when is it appropriate to add covariates?
Popular Question 23 months ago, created a question with more than 1,000 views. For How to create empty Biopython MultipleSeqAlignment object?
Popular Question 23 months ago, created a question with more than 1,000 views. For General approach for genotype refinement after GATK processing?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For General approach for genotype refinement after GATK processing?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For General approach for genotype refinement after GATK processing?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Hardy-Weinberg assumptions in variant calling
Scholar 3.2 years ago, created an answer that has been accepted. For A: Can NUCmer align a short sequence with a much longer sequence (local alignment)?
Supporter 3.2 years ago, voted at least 25 times.
Popular Question 3.5 years ago, created a question with more than 1,000 views. For GWAS: when is it appropriate to add covariates?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Best way to convert VCF to PLINK file format and merge chromosomes?
Student 4.3 years ago, asked a question with at least 3 up-votes. For GWAS: when is it appropriate to add covariates?

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