Journals, Conferences, and References
Journals, Conferences, and References
Genomic data analysis, A good analysis tool Bioconductor. Purdue HPC, Anvil login link is here. Data transfer can use globus from local computer to HPC.
Bulk RNA sequencing, reference Yun, et al. The data was deposited to NCBI GEO as GSE80609, at the end of the SRA run selector, also at Sequence Read Archive. SRA maintains the sratoolkit, fastq-dump documentation, SRAToolkit instructions here. Trimming reads reference (see Zhou and Rokas), download and install following this website. For additional information on Trimmomatic, see the Trimmomatic website or the Bioinformatics paper. The STAR article in Bioinformatics or the STAR Github repository. The human GRCh38 annotation FASTA file can be downloaded from Ensembl FTP download website
Single cell RNA sequencing, Vickman et al. Preprocessing using Cell Ranger, quality control using Seurat, more information about Seurat on Satija Lab, some discussion on sequencing noise here, feature variable selection is here. Sample data download here.
GWAS, plink generate a number of standard summary statistics that are useful for quality control
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