Transcriptomics - Genomics

Transcriptomics

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,

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. >>>

A multi-tiered RNA-seq analyses approach to clinical diagnosis of a genetic disease

A novel three-tiered approach of targeted RNA-seq analysis for molecular diagnosis of a genetic disease (ex. neuromuscular disease; NMD) was proposed. Analysis will be stopped if molecular diagnosis is achieved in any of the Tiers and the results will be clinically correlated to reclassify variants of uncertain significance (VUSs), identify pathogenic events at the mRNA

RNA-Seq : raw reads to differential expression

A simple RNA-Seq differential expression analysis using High Performance Computing (HPC). >>>

Genomic variants from RNA-seq data

RNA-Seq allows the detection and quantification of known and rare RNA transcripts within a sample. In addition to differential expression and detection of novel transcripts, RNA-seq also supports the detection of genomic variation in expressed regions. >>>