by Amit | Jun 10, 2019 | Bioinformatics
Sometimes popular NGS analysis pipelines aren’t enough, and your team needs a custom solution. EpiCypher, a biotech company that develops cutting-edge technologies for epigenetic and chromatin biology, needed a specialized pipeline built for their internal team and...
by Amit | Apr 11, 2019 | Bioinformatics
Audits are probably the most dreaded aspect of NGS data analysis, and like specters, they come in many forms to haunt you. You might need to publish results from several years back, only to realize that the open source tools you used have dramatically changed, forcing...
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...
by Stuart Davis | Aug 27, 2018 | Bioinformatics
The performance of NGS alignment tools has continuously improved, but sorting the aligned data now takes more time than alignment. A big leap in sorting was recently initiated with SAMtools version 1.x, with support for parallel processing for sorting. We compared the...
