#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***
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 email@example.com 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.
|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!