We are actively working on the homework for sessions 2 and 3! 🙂
The 4th session to run on next Monday (Oct. 15) 1-3pm. Hope it works for you! The revised course topics are as follows:
|NAT1||9/11-12/18||10am-||T4007,LectureD||Introduction (library prep – sequencing), useful unix commands|
|NAT2||9/18,20/18||1pm-, 10am-||C2609D||FastQC, Fastq filtering, RNA-seq alignment, Cufflinks|
Transcript assembly-novel finding, More analysis by R;differential gene expression (other than Cufflinks), venn diagram
manipulating more on.bam; QC Picard, visualizing in IGV, UCSC track, smRNA-seq
|NAT5||week of 10/29/18||TBD||C2609D||Exome alignment, variant calling, variant annotation|
|NAT6||week of 11/12/18||TBD||C2609D||reviewing NAT4-5 homework, SRA, dbGap, TCGA|
|NAT7||week of 11/26/18||TBD||C2609D||Amplicon seq, CRISPR screening, ChIP-seq, peak calling, differential binding analysis|
|NAT8||week of 12/10/18||TBD||C2609D||Methyl-seq, DMR analysis, Metagenome 16S, shotgun WGS|
|HW submission deadline||12/31/18|
3 directly irrelevant but useful announcements:
(1) for those that have used 3’mRNAseq (aka Quantseq, or $100 RNAseq 🙂 technologies (like Irina), the vendor (bluebee) provides free analysis platform that runs by GUI. They happened to be running a webinar on it, so I’d encourage the existing or future 3’mRNAseq users to take this.
(2) I plan to run similar hands-on using the 3’mRNAseq and the bluebee’s GUI platform in Pharmacology seminar on 18th (Thursday, from 4pm) so you are welcome to attend this one too!
(3) Research Core will be running a first annual symposium this Wednesday (Oct. 10) 9am – 3pm at UCC. Free food! and 4 lightning talks from my users including Steve Hicks and Lucian Moldovan!
Thank you for voting for the sessions 1 and 2! To fit most of the participants’ schedules, I would run 2 alternative timings for each of session 1 and 2! Namely… session 1 to be run on 9/11 (Tue) 10-1130 and on 9/12 (Wed) 10-1145, and then session 2 on 9/18 (Tue) 1-3 at and 9/20 (Thu) 10-12. Please try to attend one each and we will be good to go in terms of setting up accounts and running introductory command-line practices. More details to be found from the Google Classroom for those signed up there already or to be emailed directly to Yuka. Thank you!
|NAT1||9/11-12/18||10am-||Introdutoin (library prep – sequencing), useful unix commands|
|NAT2||9/18,20/18||1pm-, 10am-||FastQC, Fastq filtering, RNA-seq alignment, Cufflinks|
|NAT3||week of 10/1/18||TBD||smRNA-seq, RNA-seq; manipulating more on.bam; QC Picard, visualizing in IGV, UCSC track|
|NAT4||week of 10/15/18||TBD||More analysis by R;PCA,heatmap,etc, differential gene expression (other than Cufflinks)|
|NAT5||week of 10/29/18||TBD||Exome alignment, variant calling, variant annotation|
|NAT6||week of 11/12/18||TBD||reviewing NAT4-5 homework, SRA, dbGap, TCGA, homework review|
|NAT7||week of 11/26/18||TBD||Amplicon seq, CRISPR screening, ChIP-seq, peak calling, differential binding analysis|
|NAT8||week of 12/10/18||TBD||Methyl-seq, DMR analysis, Metagenome 16S, shotgun WGS|
|HW submission deadline||12/31/18|
Doodle poll for 1st session: Thanks a lot for taking the survey! Regarding the timing, I’m finding Wednesdays and mornings are most popular, however, since the 1st session is the most important to get you set up at our analysis server, I’d like to take your vote again and see which date/time would most fit your schedule. I’m thinking to throw the 1st session in the week of 9/10. Thank you!
I will be again offering sessions on data analysis for nextgen sequencing (aka NAT_3rd: NGS Analysis Training 3rd season).
The group will be gathering every 2 weeks starting from September for a total 8 times of hands on tutorial sessions which will run ~2 hrs and the participants will be given a homework after each session. A certificate will be given to whom complete the minimum number (to be determined) of homework! If interested, please let me know by email firstname.lastname@example.org.
Please also take the below survey so that I can better plan for the programs.