by Rohan Sharma | Sep 27, 2022 | Bioinformatics
One of the pioneering medical device companies specializing in IVF (In Vitro Fertilization) found itself at a crossroads. They already had a multi-billion dollar portfolio of instruments, assays, and culture media and decided to expand their portfolio to include a...
by Rohan Sharma | Sep 12, 2022 | Bioinformatics
Is it necessary to do base quality score recalibration (BQSR) in the GATK pipeline? How should this be done without an available vcf file of known sites? (a) Unfortunately the quality scores produced by next generation sequencing instruments are subject to various...
by Rohan Sharma | Aug 27, 2022 | Bioinformatics
Cell and Gene Therapy Biotechnology Company Case Study Time is everything for a bioinformatician. With an active R&D group constantly creating new datasets that need to be analyzed, keeping up with their requests is an uphill battle. The newly hired...
by Amit | Mar 22, 2021 | Bioinformatics
NGS Data Analysis Bottlenecks One of the biggest bottlenecks in next generation sequencing (NGS) today is data analysis, which is surprising considering that we have massive compute available at our fingertips, the available infrastructure to process thousands of...
by Stuart Davis | Oct 26, 2019 | Bioinformatics
Trimming for adaptors and low quality bases is important part of the analysis pipeline for sequencing data. Typically, after you isolate and fragment your RNA sample, adaptors are attached to the ends of the sequences that are needed for sequencing (see [1,2] for more...
by Stuart Davis | Mar 5, 2019 | Bioinformatics
Background One of the most popular tools for pathway enrichment analysis for RNA-seq and microarray data is the Gene Set Enrichment Analysis (GSEA) tool by the Broad Institute [1,2]. The database of pathways most often used with GSEA is MSigDB, also by the Broad...
