| NAT2020_plan | date | time | room | contents | |
| NAT2020_1 | 2/6/20 | Thu | 2:30pm-4:30pm | C2609D | setting up, Introduction (library prep – sequencing), useful unix commands |
| NAT2020_2 | 2/20/20 | Thu | 1pm-3pm | C2609D | HPC and slurm exercise, FastQC, Fastq filtering, RNA-seq alignment, quantification, visualization in IGV |
| NAT2020_2 | 3/5/20 | Thu | 1pm-3pm | C7619 | FPKM vs raw read counts, differential expression, pseudoalignment |
| NAT2020_4 | 4/2/20 | Thu | 2pm-4pm | C2609D | more analysis in R: PCA, tSNE, heatmap, batch correction, UCSC track, smRNA-seq |
| NAT2020_5 | 4/16/20 | Thu | 1pm-3pm | C2610 | exome alignment, variant calling, variant annotation |
| NAT2020_6 | 4/30/20 | Thu | 1pm-3pm | C2609D | public database: GEO, SRA, EGA, dbGap, TCGA, ENCODE, Allen Brain Atlas |
| NAT2020_7 | 5/14/20 | Thu | 1pm-3pm | C2609D | ChIP-seq and ATAC-seq, peak calling, annotation, visualization, intersecting, motif analysis, pathway analysis |
| NAT2020_8 | 5/28/20 | Thu | 1pm-3pm | C6616 | pending… HiC, Methyl-seq, DMR analysis, machine learning, (Metagenome 16S, shotgun WGS) anything else? |
| HW submission deadline | 6/14/20 | ||||
Our NGS Analysis Traning returns in February 2020!
The plan is to run 8 workshops every other week in a total of 4 months. Homework assignments will be given for motivated learners and they can earn a certificate if they successfully complete minimum assignments!
Please sign up to Slack for group announcements!
https://sites.psu.edu/yuka/contact-us/
channel ‘#NAT2020’ will be used for the class members and I will invite you once you sign up Slack and indicate you want to take the NAT2020 course.
Below is the final class schedule and learning objects!
| NAT2020_plan | date | time | room | contents | |
| NAT2020_1 | 2/6/20 | Thu | 2:30pm-4:30pm | C2609D | setting up, Introduction (library prep – sequencing), useful unix commands |
| NAT2020_2 | 2/20/20 | Thu | 1pm-3pm | C2609D | HPC and slurm exercise, FastQC, Fastq filtering, RNA-seq alignment, quantification, visualization in IGV |
| NAT2020_2 | 3/5/20 | Thu | 1pm-3pm | C7619 | FPKM vs raw read counts, differential expression, pseudoalignment |
| NAT2020_4 | 4/2/20 | Thu | 2pm-4pm | C2609D | more analysis in R: PCA, tSNE, heatmap, batch correction, UCSC track, smRNA-seq |
| NAT2020_5 | 4/16/20 | Thu | 1pm-3pm | C2610 | exome alignment, variant calling, variant annotation |
| NAT2020_6 | 4/30/20 | Thu | 1pm-3pm | C2609D | public database: GEO, SRA, EGA, dbGap, TCGA, ENCODE, Allen Brain Atlas |
| NAT2020_7 | 5/14/20 | Thu | 1pm-3pm | C2609D | ChIP-seq and ATAC-seq, peak calling, annotation, visualization, intersecting, motif analysis, pathway analysis |
| NAT2020_8 | 5/28/20 | Thu | 1pm-3pm | C6616 | pending… HiC, Methyl-seq, DMR analysis, machine learning, (Metagenome 16S, shotgun WGS) anything else? |
| HW submission deadline | 6/14/20 | ||||