#updated as of 8/20/18
Finally the certificates and prizes are ready for those who have completed the homework (minimum 2)! Just stop by my office (C2705) to pick them up whenever you can!
#updates as of 5/19/18
As soon as I see you sign on to the class (again, please use the specific code), I will communicate with you to confirm your # of homework already turned in and grade you based on that. If I don’t see you in the Google Classroom by next Friday (May 25) and yet I believe I have received more than 2 homework from you, I will try my best to pull out my record/email to compile the information. But I can’t guarantee I won’t make mistakes here… So bottom line: If you don’t hear from me through Google Calendar or email but you are sure you have submitted more than 2 homework, please forgive me and let me know by May 30! 🙂
#updates as of 4/4/2018:
Thursday (4/5) 1pm-3pm is the new time for the NAT8 session. Hope you can adjust your schedule and stop by the last session! Due to the time constraint, I will focus on the metagenome.
#updates as of 3/18/2018:
Hi everyone!
NAT_2nd_plan | date | time | room | contents |
NAT1 | 10/24/17 | 1pm-3pm | Introdutoin (library prep – sequencing), useful unix commands | |
NAT2 | 11/7/17 | 1pm-3pm | FastQC, Fastq filtering, RNA-seq alignment, Cufflinks | |
NAT3 | 11/20/17 | 1pm-2:30pm | smRNA-seq, RNA-seq; manipulating more on.bam; QC Picard, visualizing in IGV, UCSC track | |
NAT4 | 12/4/17 | 1pm-3pm | More analysis by R;PCA,heatmap,etc, differential gene expression (other than Cufflinks) | |
NAT5 | 1/8/18 | 1pm-3pm | Exome alignment, variant calling, variant annotation | |
NAT6 | 1/26/18 | 1pm-3pm | reviewing NAT4 homework, SRA, dbGap, TCGA, homework review | |
NAT7 | 2/8/18 | 1pm-3pm | Amplicon seq, CRISPR screening, ChIP-seq, peak calling, differential binding analysis | |
NATplus | 2/26/18-3/29/18 | – | Exercise onyour own |
Repositive->SRA->RNA-seq->
|
NAT8 | 3/30/18 | 2:30pm-4:30pm | TBD | Methyl-seq, DMR analysis, Metagenome 16S, shotgun WGS, 3rd generation sequencing? |
#updates as of 2/26/2018:
Hi everyone!
NAT_2nd_plan | date | time | room | contents |
NAT1 | 10/24/17 | 1pm-3pm | Introdutoin (library prep – sequencing), useful unix commands | |
NAT2 | 11/7/17 | 1pm-3pm | FastQC, Fastq filtering, RNA-seq alignment, Cufflinks | |
NAT3 | 11/20/17 | 1pm-2:30pm | smRNA-seq, RNA-seq; manipulating more on.bam; QC Picard, visualizing in IGV, UCSC track | |
NAT4 | 12/4/17 | 1pm-3pm | More analysis by R;PCA,heatmap,etc, differential gene expression (other than Cufflinks) | |
NAT5 | 1/8/18 | 1pm-3pm | Exome alignment, variant calling, variant annotation | |
NAT6 | 1/26/18 | 1pm-3pm | reviewing NAT4 homework, SRA, dbGap, TCGA, homework review | |
NAT7 | 2/8/18 | 1pm-3pm | Amplicon seq, CRISPR screening, ChIP-seq, peak calling, differential binding analysis | |
NATplus | 2/26/18-3/18/18 | – | Exercise on your own | |
NAT8 | week of 3/19/18 | Methyl-seq, DMR analysis, Metagenome 16S, shotgun WGS |
#updates as of 1/8/2018:
Happy 2018 to everyone!
NAT5 | 1/8/18 | 1pm-3pm | Exome alignment, variant calling, variant annotation |
#updates as of 11/28/2017:
Some unlucky folks have run into a memory issue and couldn’t complete jobs. Sorry! Research IT did a quick fix by expanding our computational resources! Thank you!!! Now we have 5 servers: comtrain, comtrain2, comtrain3, comtrain4, comtrain5 and everyone got assigned to each server to reduce the traffic jam 🙂
The 4th session will take place on 12/4 (Mon) from 1pm to 3pm at Crescent. Please find the room # from the Group email.
I’m also scheduling a follow up office hours for those just joined the Group or who wish to have more hands-on training with me! 🙂 A new Doodle poll invitation was just sent to the Group so please vote if you are interested in!
#updates as of 11/17/2017:
The 2nd session went with successful Tophat and Cufflinks demonstration and first homework was assigned! Looking forward to finding your answer of “magic #” of differentially expressed gene counts by Monday (11/20) 9am!
The 3rd session will take place on 11/20 (Mon) from 1pm to 2:30pm at Crescent! Please find the room # from the Group email. I will open the Doodle poll for the 4th week as well! This will be the last session before Christmas/New Year holiday.
***Remote Desktop option to work away from office***
https://sites.psu.edu/yuka/remote-access-vpn/
Hope this helps!!!
#updates as of 10/31/2017:
The 2nd session will take place on 11/7 (Tue) from 1pm to 3pm at Crescent! Please find the room # from the Group email. The Doodle poll is open for the 3rd week as well! This will be tricky week due to Thanksgiving holiday but hope we can find a best option!
#updates as of 10/26/2017:
The 1st session was a lot of FUN! Thank you so much for coming over to UCC (it was a beautiful fall day so hope everybody enjoyed a nice 10 min walk!). It was my bad didn’t know how to set up the room bigger so sorry that the room was jam-packed… Yesterday I spent 2 hours to book bigger rooms in Crescent for the coming sessions so hope that helps! Also, I will close the Doodle poll for the week 2 session today and pick the best timing for the 2nd session.
*****TODAY at 11am!!!!!***** Mark, Destiny, and Lu from IT will be running a zoom session on a Linux tutorial for those who have missed the 1st session and who need more help in Linux commands. Please find the link from the Google Group email!
#updates as of 10/24/2017:
Wow! More than 50 people signed up! and 30+ will be able to make it to the first session. Thank you! and sorry for those who can’t make it to the first session. I just created a Google Groups and sent an invitation to everyone. I will share presentation materials, example commands, homework assignments etc. through the NAT_2nd Group. If you have any questions or requests, please send message through the NAT_2nd Group.
See you at 1pm!
#updates as of 10/17/2017:
#updates as of 10/2/2017:
I sent out Doodle poll requests to those who RSVP’ed by email. Almost 50 interested people so far! I might have missed your email so please get back to me if I you didn’t get the Doodle poll invitation.
#email invitation sent out to Hershey scientists/students in late September:
The Genome Sciences Core will be again offering sessions on data analysis for nextgen sequencing.
The small group will be gathering every 2 weeks starting from mid-late October 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 all the homework! This is hands-on tutorial and space is limited so the preference will be given to new learners who has already sequenced something with us. If interested and can commit to the 8 times of sessions, please send me an email yimamura@pennstatehealth.psu.edu and we will run a Doodle Poll to pick dates/times. Even if you cannot commit to all 8 sessions, you are welcome to attend particular session of your most interest, if space allows!
Below is a tentative plan for the 2nd season.
NAT_2nd_plan | date (TBA) | contents |
NAT1 | 10/24/17 (Tue) 1pm-3pm | Introdutoin (library prep – sequencing), useful unix commands |
NAT2 | 11/7/17 (Tue) 1pm-3pm | FastQC, Fastq filtering, RNA-seq alignment, Cufflinks |
NAT3 | 11/20/17 (Mon) 1pm-2:30pm | smRNA-seq, RNA-seq; manipulating more on.bam; QC Picard, visualizing in IGV, UCSC track |
NAT4 | 12/4/17 (Mon) 1pm-3pm | Reviewing NAT2/NAT3 homeworks…More analysis by R;PCA,heatmap,etc, differential gene expression (other than Cufflinks) |
NAT5 | 1/8/18 | Exome alignment, variant calling, variant annotation |
NAT6 | week of Jan22 | SRA, dbGap, TCGA, Amplicon seq, CRISPR screening |
NAT7 | week of Feb5 | ChIP-seq, peak calling, differential binding analysis, Methyl-seq, DMR analysis |
NAT8 | week of Feb19 | Metagenome 16S, shotgun WGS |
Thank you so much!
Yuka