User: tjduncan

gravatar for tjduncan
tjduncan270
Reputation:
270
Status:
Trusted
Location:
Indianapolis, IN
Twitter:
TD_DNA
Last seen:
1 week, 2 days ago
Joined:
3 years, 11 months ago
Email:
t************@gmail.com

Posts by tjduncan

<prev • 16 results • page 2 of 2 • next >
5
votes
2
answers
5.4k
views
2
answers
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 3.0 years ago by tjduncan270
1
vote
1
answer
2.8k
views
1
answers
Answer: A: Version history and design files for exome kits from Agilent, Roche(Nimblegen),
... Hi, This is a great list of exome capture providers to use as future reference. I included a bit of info on two additional exome capture providers in the message below. One of the biggest "up and coming" exome capture providers is IDT. Many users are very familiar with them for their other oligo w ...
written 3.1 years ago by tjduncan270
1
vote
4
answers
1.7k
views
4
answers
Answer: A: Sanger sequencing is no longer the gold standard?
... See the white paper below from Invitae on their confirmation methods. They must be doing something right as they have doubled their revenues during the last quarter: https://www.genomeweb.com/molecular-diagnostics/invitae-more-doubles-q3-revenues They talk about the orthogonal methods they use to c ...
written 3.1 years ago by tjduncan270
2
votes
3
answers
1.5k
views
3
answers
Answer: A: Pacbio sequencing database
... The NCBI and EMBL-ENA databases are great for all types of public access data. Specifically to answer your question, the best and most comprehensive database for PacBio microbial data is the NCTC 3000 collection. Per their website: "NCTC 3000 is a collaborative Whole Genome Sequencing (WGS) proj ...
written 3.1 years ago by tjduncan270
5
votes
1
answer
2.1k
views
1
answers
Answer: A: How to calculate the different expression gene used PacBio full-length cDNA seq
... Since you don't have a reference genome/transcriptome you would need to generate your sample specific genemodels (ie: generate your own reference transcriptome from your pacbio data) then quantify the expression levels of your illumina data using your newly generated pacbio reference transcriptome w ...
written 3.1 years ago by tjduncan270
1
vote
2
answers
2.3k
views
2
answers
Answer: A: Assembling PacBio reads using a reference genome
... "Long-read sequencing improves assembly of Trichinella genomes 10-fold, revealing substantial synteny between lineages diverged over 7 million years." https://www.ncbi.nlm.nih.gov/pubmed/28583210 In this recent paper they do something similar to what I believe you are looking to do. They take a sh ...
written 3.3 years ago by tjduncan270

Latest awards to tjduncan

Teacher 22 months ago, created an answer with at least 3 up-votes. For A: PacBio interpulse duration (IPD) data
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: PacBio interpulse duration (IPD) data
Scholar 2.5 years ago, created an answer that has been accepted. For A: PacBio interpulse duration (IPD) data
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: PacBio interpulse duration (IPD) data
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: PacBio interpulse duration (IPD) data
Scholar 2.7 years ago, created an answer that has been accepted. For A: How to calculate the different expression gene used PacBio full-length cDNA seq
Scholar 3.1 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 3.1 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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1357 users visited in the last hour