User: tjduncan

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tjduncan250
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250
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Indianapolis, IN
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TD_DNA
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3 weeks, 6 days ago
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2 years, 11 months ago
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Posts by tjduncan

<prev • 15 results • page 1 of 2 • next >
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Answer: A: PacBio sequencing for variant calling?
... Hi All, What the others have said is generally accurate. Typically Illumina short read data is great for SNPs and long read data (PacBio or ONT) is typically used (this is changing) primarily for de novo assemblies or structural variation. If you truly have a good reference genome your idea of mapp ...
written 10 months ago by tjduncan250
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Tool: Interactive global map of human genome assemblies that use long read sequencing (PacBio) data.
... Hey All, I wanted to share a resource/tool that was put together regarding human genome reference assemblies. This interactive map showcases global initiatives underway to generate reference quality human genome assemblies for diverse populations using long read (PacBio) data. This is interesting b ...
wgs assembly tool human pacbio written 15 months ago by tjduncan250
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Answer: A: PacBio methylation information in bam file
... I have complied some of the steps to do this in a previous post. I am not an expert on this by any means but most of PacBio's official documentation for this type of pipeline is outlined in the post linked below: https://www.biostars.org/p/302290/#302647 ...
written 18 months ago by tjduncan250
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Comment: C: PacBio long read error correction tools
... What is the scientific/biological question you are looking for an answer to? Depending on your question there are different initial error correction bfx pipelines that are reccomeded for PacBio data. ...
written 20 months ago by tjduncan250
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Answer: A: PacBio interpulse duration (IPD) data
... - What organism is your data from? - What is the genome size of the organism? What Coverage do you have? - What PacBio instrument was your data generated on RSII (output is a bax.h5 file) or Sequel (output is an unaligned .bam file)? The instrument that the data was generated on is important as ...
written 20 months ago by tjduncan250
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Answer: A: mpileup for PacBio reads
... I think that taking a look at the recent biorxiv paper may answer some questions... but significantly complicate things... - **New synthetic-diploid benchmark for accurate variant calling evaluation** https://www.biorxiv.org/content/early/2017/11/22/223297 Unfortunately I don't know of a great met ...
written 23 months ago by tjduncan250
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Answer: A: SNP calling for correcting errors ?
... The Hercules package that hit biorxiv recently may be perfect for this. It is a profile HMM-based hybrid error correction algorithm for long reads. https://www.biorxiv.org/content/early/2017/12/13/233080 https://github.com/BilkentCompGen/Hercules ...
written 23 months ago by tjduncan250
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Answer: A: long reads Pacbio SNP calling
... If you have 200x coverage of a microbe you should just make a de novo assembly with your data using a long read assembler. The two I would recommend are HGAP4 or Canu. Both of these assemblers include a consensus step and will yield an assembly that is of high enough quality to do SNP based variant ...
written 23 months ago by tjduncan250
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Answer: A: NGS Project report formate for a Post graduate level student.
... I recently had to do a final project for my STAT555 class at PSU. The title of my report was: Reproducible Bioinformatics: RNA-Seq Differential Expression Analysis of West Nile Virus Infection in the Zebra Finch. The way the report was organized is outlined below (this is copied streight from the gr ...
written 23 months ago by tjduncan250
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Answer: A: PacBio Reads subreads and scraps files
... For assembly you would only need the "Subreads.bam". You would only need the scraps.bam if you had multiplexed samples in your data-set that needed to have their barcodes identified to be de-multiplexed via CCS. See: [Brief primer and lexicon for PacBio SMRT sequencing][1] for more info on file ...
written 2.0 years ago by tjduncan250

Latest awards to tjduncan

Teacher 10 months ago, created an answer with at least 3 up-votes. For A: PacBio interpulse duration (IPD) data
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: PacBio interpulse duration (IPD) data
Scholar 18 months ago, created an answer that has been accepted. For A: PacBio interpulse duration (IPD) data
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: PacBio interpulse duration (IPD) data
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: PacBio interpulse duration (IPD) data
Scholar 20 months ago, created an answer that has been accepted. For A: How to calculate the different expression gene used PacBio full-length cDNA seq
Scholar 2.1 years ago, created an answer that has been accepted. For A: How to calculate the different expression gene used PacBio full-length cDNA seq
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: How to calculate the different expression gene used PacBio full-length cDNA seq

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