![]() ![]() (The software is expected to run without problem on other recent Linux systems, but we do not guarantee this.) 8 GB RAM required 16 GB RAM recommended 1024 x 768 display required 1600 x 1200 display recommended Intel or AMD CPU required 500GB disc space required in the CLC Genomics serverġ8 HPC Partnership with CRC to Mitigate Computational Bottleneck ![]() Introduction to clc genomics workbench windows#System Requirements Windows Vista, Windows 7, Windows 8, Windows 10, Windows Server 2012 or 2016 Mac: OS X 10.10, and macOS 10.12, 10.13, 10.14 Linux: RHEL 7 and later, Suse Linux Enterprise Server 11 and later. 1 Bulk RNA-Seq Analysis Using CLCGenomics WorkbenchĢ019 Ansuman Chattopadhyay, PhD Asst Director, Molecular Biology information service Health sciences library system University of pittsburgh Sri Chaparala, MS Bioinformatics Specialist Health Sciences Library System University of PittsburghĢ Topics Brief introduction to RNA-Seq experiments Analyze RNA-seq dataĭownload seq reads from EBI-ENA/NCBI SRA Import reads to CLC Genomics Workbench Align reads to Reference Genome Estimate expressions in the gene level Estimate expressions in the transcript isoform level Statistical analysis of the differential expressed genes and transcripts Create Heat Map, Volcano Plots, and Venn Diagramĭescriptions & Registration: 4th Single Cell RNA-Seq 10-11am Genomics Research Core 11am-12pm Overview 1-3pm Hands-On SEPTEMBER 11th ChIP-Seq & CLC Genomics 10am-12pm Overview & 1-3pm Hands-On 25th Pathway Analysis-IPA & MetaCore 10am-12pm Overview & 1-3pm Hands-On 2nd Bulk RNA-Seq 10-11am Genomics Research Core 11am-12pm Overview 1-3pm Hands-On Fall 2019 HSLS MolBio Workshops OCTOBER 9th Pathway Analysis-Open Access Tools 10am-12pm Overview & 1-3pm Hands-On 23rd ChIP-Seq & Partek Flow 1-4pm 30th Gene Regulation 1-4pm Scaife Hall, Falk Library, Classroom 2 6th Single Cell RNA-Seq 10am-12pm Overview & 1-3pm Hands-On NOVEMBER 13th Gene Expression Visualization 1-4pm 20th Pathway Analysis-IPA & MetaCore 10am-12pm Overview & 1-3pm Hands-On 4th Bulk RNA-Seq 10-11am Genomics Research Core 11am-12pm Overview 1-3pm Hands-On DECEMBER 11th Genetic Variation 10am-12pm Overview & 1-3pm Hands-Onĩ Partek Flow : Software for scRNA-Seq Data AnalysisĮnrichment Analysis Deferentially Expressed Genes CLC Genomics Work Bench Ingenuity Pathway Analysis Functions Diseases Pathways Key Pathway Advisor Upstream Regulators Volcano Plot PCA Plot Venn Diagram Heat Map Any Organism Illumina BaseSpace Correlation Engine RNA-Seq Reads RNA-Seq Analysis Down Stream Analysisġ2 RNA-Seq Data Analysis Support through HSLS MBISġ3 RNA Seq Questionnaire What is the scientific objective of the RNA Seq experiment? How many classes will be compared? Are only coding RNA (mRNA) or long non coding RNA, miRNA expected to be detected? Did all the samples pass RNA quality checks before sequencing? Are there biological replicates? If so how many? What type of sequencing platform was used to sequence the reads? Illumina, Ion torrent, Solid Where was the sequencing performed? Facility name and contact info When was the sequencing performed? Year/date Which RNA – extraction method was used in the experiment? Total RNA/ poly A/ rRNA depletion method and kit name and if possible, link to protocol Whether the protocol is strand specific or not? Unstranded/ forward/reverse, kit name and if possible link to protocol Whether the data is single end or paired end? What is the expected read length? Do the reads contain adapters or removed? If not please provide adapter sequence, if available, or link (usually can get this info from facility) What are the experimental conditions to perform differential expression analysis? Which organism and the reference genome to be used for analysis?ġ5 CLCGx 12 Genomics Workbench BioMedical Workbench ![]()
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