Ashok Dinasarapu - Genomics

Ashok Dinasarapu

Spatial gene expression data analysis on Cluster : 10X Genomics, Space Ranger

Running spaceranger as cluster mode that uses Sun Grid Engine (SGE) as queuing. There are 2 steps to analyze Spatial RNA-seq data. Step 1: spaceranger mkfastq demultiplexes raw base call (BCL) files generated by Illumina sequencers into FASTQ files. Step 2: spaceranger count takes FASTQ files from spaceranger mkfastq and performs alignment, filtering, barcode counting,

Taxonomic and functional profiling of the microbiome – whole genome shotgun metagenomics

This workflow consists of taxonomic and functional profiling of shotgun metagenomics sequencing (MGS) reads using MetaPhlAn2 and HUMAnN2, respectively. To perform taxonomic (phyla, genera or species level) profiling of the MGS data, the MetaPhlAn2 pipeline was run on a high performance multicore cluster computing environment. >>>

Taxonomic and diversity profiling of the microbiome : 16S rRNA gene amplicon sequence data

The 16S ribosomal RNA (rRNA) gene of Bacteria codes for the RNA component of the 30S subunit. Different bacterial species have one to multiple copies of the 16S rRNA gene, and each with 9 hypervariable regions, V1-V9. High-throughput sequencing of 16S rRNA gene (a “marker gene”) amplicons has become a widely used method to study

Building a real-time big data pipeline 9: Spark MLlib, Regression, Python

Apache Spark expresses parallelism by three sets of APIs – DataFrames, DataSets and RDDs (Resilient Distributed Dataset).Originally, spark was designed to read and write data from and to Hadoop Distributed File System (HDFS). A Hadoop cluster is composed of a network of master, worker and client nodes that orchestrate and execute the various jobs across

Single cell gene expression data analysis on Cluster : 10X Genomics, Cell Ranger

Cell Ranger can be run in cluster mode, using job schedulers like Sun Grid Engine (or simply SGE) or Load Sharing Facility (or simply LSF) as queuing system allows highly parallelizable jobs. >>>