Some next generation sequencing (NGS) analyses are “frequently requested”, for these established and commonly utilized software are utilized (for example, see Table below). Some requests are “routinely-unique”, for these we also use, open source software which are peer-reviewed and published in PubMed; when there is a need to develop new workflows, the R+D is performed and new workflows are developed and utilized (for example, NET-seq, RIBO-seq). Many of the workflows utilize snakemake/nextflow frameworks. All datasets for the projects undergo quality control assessments.
Table below shows some frequently requested NGS analyses.
|QC, gene expression, gene differential expression||STAR, HTSeq-count, DEseq2|
|Single-cell RNA-seq||QC, identify highly variable genes, marker identification, cluster annotation, trajectory inference, composition analysis, differential analysis||STAR, Cell Ranger, Loupe Browser, Seurat|
|QC, germline mutation profiling, somatic mutational profiling||BWA mem, GATK4 (germline), GATK4 Mutect2 (somatic)|
|ChIP-seq||QC, chIP-seq peak-calling and differential analysis||Bowtie2, MACS2, HOMER, deepTools, ChIPpeakAnno|
|ATAC-seq||QC, ATAC-seq peak-calling and differential analysis||Bowtie2, MACS2, HOMER, deepTools|
|Methyl-seq||QC, bisulfite-sequencing to characterize the methylome (hyper methylated or hypo-methylated regions of the genome)||Bowtie2, Bismark, Metilene|