Hi all, I am preparing a course on NGS: there will be seven students for 4 hours an I want them to play with some NGS data. No programming skill is required here.
Here is what I plan to do:
my other ideas:
Any other suggestion ? What would you like to see during this course ?
I'll validate the answer with highest number of votes next week.
EDIT: the course should give them the opportunity see what would look the work of someone working with NGS and to have an experience with some real data. I don't know their skill but AFAIK, there are supposed to have some programming courses later.
My only experience is the analysis of "exome capture" data = SNP.
Update: I posted my slides on slideshare: http://www.slideshare.net/lindenb/20101210-ngscourse
asked 21 May '12, 16:40
Titus Brown at Michigan State University has run a course on Analyzing Next Generation Sequencing Data and as the link shows he has built an amazing resource around it.
His tutorials might give you a good sense on what topics to include and what level of detail may be appropriate.
answered 21 May '12, 16:40
It is important to let students play with real or simulated data.
EDIT: a further comment:
I used to give a two-hour course on variant discovery. I gave each attendee a tar-ball which includes a bacterial genome (S. suis), a variant/read simulator (wgsim), a mapper (bwa), a SNP caller (samtools) and a few scripts. It is only a couple of MB in size, suitable for email. With these, one can do simulation, mapping, SNP calling, visualization and evaluation, nearly the entire pipeline. I have lost the tar-ball, though.
answered 21 May '12, 16:42