User: nchuang

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nchuang190
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5 months ago
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3 years, 9 months ago
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Posts by nchuang

<prev • 67 results • page 1 of 7 • next >
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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 5 months ago by nchuang190
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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 5 months ago by nchuang190
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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 5 months ago by nchuang190
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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 5 months ago by nchuang190 • updated 5 months ago by Antonio R. Franco4.0k
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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 18 months ago by nchuang190
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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 18 months ago by nchuang190
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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 18 months ago by nchuang190
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VIew reads sorted by name in IGV
... I have two sets of alignments from different sequencing runs that I want to compare in IGV. I want to maintain the order of the read alignments between the two bams so I can visually compare the alignments, but when I sort the bams I lose the order. I know I can use samtools sort -n but then I can't ...
bam samtools igv written 18 months ago by nchuang190 • updated 18 months ago by d-cameron2.0k
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Is it possible to map prior to Pregap4 and Gap4?
... I sanger sequenced many reads with primers that I know the correct order. I mapped the reads to the reference sequence using bowtie. I found that Pregap4 and Gap4 have excellent manipulation and visualization of sequences and chromatograms. The only annoying thing is I have to denovo assemble each t ...
staden gap4 pregap4 written 18 months ago by nchuang190
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Assemblying Sanger traces and error threshold
... I am new to working with Sanger traces and have been struggling with figuring out how to best assemble my sequences with them. I have been using lh3's seqtk trimfq for Phred based trimming. I essentially start at 0.05 error threshold and manually check if traces at the ends look good enough. If not, ...
sanger abi assembly written 21 months ago by nchuang190

Latest awards to nchuang

Popular Question 5 months ago, created a question with more than 1,000 views. For How to setup Vi or Vim in Cygwin?
Appreciated 14 months ago, created a post with more than 5 votes. For GWAS: when is it appropriate to add covariates?
Popular Question 14 months ago, created a question with more than 1,000 views. For How to create empty Biopython MultipleSeqAlignment object?
Popular Question 14 months ago, created a question with more than 1,000 views. For General approach for genotype refinement after GATK processing?
Popular Question 20 months ago, created a question with more than 1,000 views. For General approach for genotype refinement after GATK processing?
Popular Question 21 months ago, created a question with more than 1,000 views. For General approach for genotype refinement after GATK processing?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Hardy-Weinberg assumptions in variant calling
Scholar 2.5 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 2.5 years ago, voted at least 25 times.
Popular Question 2.8 years ago, created a question with more than 1,000 views. For GWAS: when is it appropriate to add covariates?
Popular Question 2.8 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 3.6 years ago, asked a question with at least 3 up-votes. For GWAS: when is it appropriate to add covariates?

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