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Mohammed Khalfan

Shared Genome Resource
Bioinformatics

Explore the New Shared Genome Resource

Save time and resources with the local CGSB repository of commonly used genomic data sets. Data is obtained from Ensembl and NCBI. New versions/releases will be added periodically or upon request. Previous versions/releases will be preserved. All files are readable from within the shared genome resource. There is no need Read more…

By Mohammed Khalfan, 8 years2017-07-05 ago
Bioinformatics

Remote Desktop Connection to Prince

Connect to Prince using a remote desktop to analyze your data in RStudio, visualize in IGV, and interact with other GUI applications on the HPC.

By Mohammed Khalfan, 8 years2017-06-21 ago
Salmon and kallisto
Bioinformatics

Salmon & kallisto: Rapid Transcript Quantification for RNA-Seq Data

Salmon and kallisto might sound like a tasty entree from a hip Tribeca restaurant, but the duo are in fact a pair of next-generation applications for rapid transcript quantification. They represent a new approach to transcript quantification using NGS that has a number of advantages over existing alignment-based methods. I’ve Read more…

By Mohammed Khalfan, 9 years2016-06-15 ago
Bioinformatics

Node to Joy: Maximize Your Performance on the HPC

In this post we’ll discuss maximizing your performance on the HPC. This entry is aimed towards experienced HPC users; for new users, please see Getting Started on the HPC. Recent advances in sequencing technology have made High Performance Computing (HPC) more critical than ever in data-driven biological research. NYU’s HPC Read more…

By Mohammed Khalfan, 9 years2016-04-26 ago
SNPs in IGV
Bioinformatics

Variant Calling Pipeline: FastQ to Annotated SNPs in Hours

Update: This pipeline is now deprecated. See the updated version of the variant calling pipeline using GATK4. Identifying genomic variants, such as single nucleotide polymorphisms (SNPs) and DNA insertions and deletions (indels), can play an important role in scientific discovery. To this end, a pipeline has been developed to allow Read more…

By Mohammed Khalfan, 9 years2016-03-09 ago

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