Next-Gen Sequencing

I just finished a revised genome assembly for a collaborating lab.  We do de novo sequencing of bacterial genomes all the time, sometimes in batches of 50 or 100 different isolates barcoded toge...

http://nextgenseq.blogspot.com/2018/10/some-tips-to-optimize-bacterial-genome.html

There are many excellent tools for analysis of Next Gen Sequencing data in the standard BAM alignment format so I was surprised how difficult it was for me to get a nice graph of genome coverage....

http://nextgenseq.blogspot.com/2018/01/genome-coverage-from-bam-file.html

Public databases of genetic information have a fundamental garbage-in>garbage-out problem. A huge number of useful databases are populated by pulling information from other databases and adding ...

http://nextgenseq.blogspot.com/2018/01/genome-annotation-challenges.html

This is a long post, so first a quick summary. SOME GENOME SEQUENCES CONTAIN CONTAMINANTS. These contaminants create many problems when we use a trusted resource like GENBANK or UNIPROT to summar...

http://nextgenseq.blogspot.com/2017/12/contaminated-genomes.html

Together with Ike Wirgin in the NYUMC Dept. of EnvironmentalMedicine , we just published a paper on a gene expression study of a fish population in the Hudson River in Genome Biology and Evolut...

http://nextgenseq.blogspot.com/2017/08/gene-expression-analysis-shows-that.html

I spend a lot of time answering questions from researchers working with genomic data. If I put a lot of effort into an answer, I try to keep it in my file of 'Frequently Asked Questions' - even t...

http://nextgenseq.blogspot.com/2017/07/rna-seq-power-calculation-faq.html

We have been testing out the Oxford MinION  DNA sequencing machine to see what it can contribute to larger de novo sequencing projects.  Most of the posted data so far come from small genomes w...

http://nextgenseq.blogspot.com/2017/02/oxford-minion-1d-and-2d-reads.html

A nice review of my 2015 Coffee Beetle paper in GenomeWeb today. My genome had 163 million bases and 19,222 predicted protein-coding genes. I am very pleased to learn that a revised version of...

http://nextgenseq.blogspot.com/2017/01/genomeweb-reports-on-updated-coffee.html

This work was conducted mostly by my research assistant Yuhan Hao . We have recently been using Bowtie2 for sequence comparisons related to shotgun metagenomics, where we directly sequence sa...

http://nextgenseq.blogspot.com/2016/12/finding-differences-between-bacterial.html

A number of groups at our research center have recently become interested in metagenomic shotgun sequencing (MGS), which is simply taking samples that are presumed to contain some microbes, extr...

http://nextgenseq.blogspot.com/2016/05/functional-metagenomics-from-shotgun.html

I get frustrated by the lack of stability in genomics data collection and analysis, which of course leads to irreproducible results. I imagine (naively I'm sure) that in physics one measures a qu...

http://nextgenseq.blogspot.com/2016/03/irreproducible-results.html

We ran a tutorial at NYU Med Center last week on the basics of RNA-seq data analysis. This tutorial was based on the use of our High-Performance Linux cluster, so we actually presented the class...

http://nextgenseq.blogspot.com/2016/02/rna-seq-workshop.html

There was a lot of publicity back in November about the genome sequence of theTardigrade (Hypsibius dujardini ), a small animal (0.05 – 1mm) that is somewhat similar to nematodes. These are fa...

http://nextgenseq.blogspot.com/2016/01/the-tardigrade-miscalculation.html

I've been reading a bit about the "Cancer Moonshot" discussion at the Davos economics conference. http://www.weforum.org/events/world-economic-forum-annual-meeting-2016/sessions/cancer-moonshot...

http://nextgenseq.blogspot.com/2016/01/cancer-moonshot-in-cloud.html

We are starting a new Masters program in Biomedical Informatics at NYU School of Medicine in 2016.  We currently have about a dozen PhD students, but the Masters program is intended to serve a w...

http://nextgenseq.blogspot.com/2015/10/masters-in-biomedical-informatics-at.html

At NYU, first-year PhD students in the Sackler Institute  start their first semester with a week-long full-time "Research Adventure" workshop.  I was asked (at short notice) to mentor a group o...

http://nextgenseq.blogspot.com/2015/09/research-adventure-with-encode-data.html

Our paper on the de novo genome sequence and annotation of the Coffee Berry Borer (a beetle) is published today in Nature Scientific Reports . This was a really fun project, where I was pushed t...

http://nextgenseq.blogspot.com/2015/07/coffee-berry-borer-genome-published.html

I am writing new lectures and organizing a lot of teaching material to teach 4 (!) classes this fall at two different universities (NYU and Fordham). I would like to keep the teaching materials i...

http://nextgenseq.blogspot.com/2015/07/i-am-writing-new-lectures-and.html

CSHL Press has made the RNA-seq chapter of my Next-Gen Seq book available free from their website: RNA Sequencing with Next-Generation Sequencing. http://www.cshlpress.org/pdf/sample/2015/next...

http://nextgenseq.blogspot.com/2015/07/cshl-press-has-made-rna-seq-chapter-of.html

The second edition of the NEXT-GENERATION SEQUENCING INFORMATICS book (that I edit) is at the printer and available for pre-order at Cold Spring Harbor Press and Amazon . We think it will ship...

http://nextgenseq.blogspot.com/2015/05/new-next-gen-seq-2-book-is-at-printer.html

This is not a Bioinformatics post, just an amusing technology catch-22 that I encountered this morning. At NYU we have automatic mandatory password updates for our accounts with IT. This includes...

http://nextgenseq.blogspot.com/2015/02/password-hell.html

We are giving a new course in the PhD program at NYU Med School (Sackler Institute) this semester called "Introduction to Biostatistics and Bioinformatics". It will have a mixture of lectures on ...

http://nextgenseq.blogspot.com/2014/09/we-are-giving-new-course-in-phd-program.html

I have been helping out several  groups who want to do cheap, quick genome projects on previously "unsequenced" eukaryotic organisms. In terms of the genetic diversity of living things, at this...

http://nextgenseq.blogspot.com/2014/08/cheap-genome-projects.html

Yesterday I attended an excellent symposium on genomic structural variation organized by the Simons Foundation . The unifying theme from all of the speakers was the use of Pacific Biosicences...

http://nextgenseq.blogspot.com/2013/11/dr-evan-eichler-speaks-about-genomic.html

One bit of followup on the Pig genome annotation story. We usually visualize RNA-seq results in the IGV browser. It allows direct inspection of read alignments to your favorite genes and can also...

http://nextgenseq.blogspot.com/2013/10/a-bit-more-on-genome-annotation.html