Yuka Imamura Kawasawa

yimamura@pennstatehealth.psu.edu

NAT_3rd

 

 

 

 

#update: 11/30/18

Next session will be the last one! and I’d like to see what else (or more to add to previous topics) you’d like to learn to conclude our training. Please go ahead and comment your thoughts/requests in the slide (page 2) or class stream!

https://docs.google.com/presentation/d/1iFba6zBVg6SCZafvQWzCHjmaLlD98esRPXGdu5r6Gro/edit?usp=sharing

NAT_3rd_plan date time room contents
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
NAT3 10/3/18 10am- C2609D Transcript assembly-novel finding, More analysis by R;differential gene expression (other than Cufflinks), venn diagram
NAT4 10/15/18 1pm- C2609D PCA, heatmap, visualizing in IGV, UCSC track, smRNA-seq
NAT5 11/1/18 10am- C2609D Exome alignment, variant calling, variant annotation
NAT6 11/19/18 10am- C2609D SRA, dbGap, TCGA
NAT7 11/28/18 10am- C2609D ChIP-seq, peak calling, differential binding analysis, CRISPR screening
NAT8 12/12/18 10am- C2609D HiC, Methyl-seq, DMR analysis, machine learning, (Metagenome 16S, shotgun WGS) anything else?
HW submission deadline 12/31/18

I also plan to open up office hours within December so you can catch up/troubleshoot before the 12/31 deadline. Stay tuned! 🙂

Thank you!

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#update: 10/8/18

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:

NAT_3rd_plan date time room contents
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
NAT3 10/3/18 10am- C2609D
Transcript assembly-novel finding, More analysis by R;differential gene expression (other than Cufflinks), venn diagram
NAT4 10/15/18 1-3pm C2609D
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.
https://twitter.com/gsfpsucom/status/1049356694504054785
(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!
https://twitter.com/gsfpsucom/status/1048932402427568128

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#update: 09/07/18

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!

Tentative plan:

NAT_3rd_plan date time contents
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

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#update: 08/29/18

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!

https://doodle.com/poll/v7c3ntu85x2brrqm

 

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I will be again offering sessions on data analysis for nextgen sequencing (aka NAT_3rd: NGS Analysis Training 3rd season).

https://sites.psu.edu/yuka/sample-page/eibdg-education-initiative-in-big-data-genomics/

https://sites.psu.edu/yuka/nat_3rd/

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 yimamura@pennstatehealth.psu.edu.

Please also take the below survey so that I can better plan for the programs.

https://www.surveymonkey.com/r/ZQV67VV

Thank you!

Yuka

 

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