intake_meeting_notes.md 2.04 KB
Newer Older
npappas's avatar
npappas committed
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51
Notes SASC project intake meeting
====

Please fill in more details or N/A if not applicable for the following questions.

### Project setup
* What is your research question?

* Please describe your study design.

* How many samples? Do the subjects have family members can be sequenced as well?

* What type of data and experiment (e.g., DNA, RNA, captured exomes, etc) are you interested in?

* For cancer project, do you have tumor normal pairs? If not, why?  

* For RNAseq project, please provide sample sheet (ref to other files in /doc)?

* Is this project part of a larger study? How do you compare with other similar project if any?

* What's your publication plan?

### If you already have generated sequencing data or have decided your sequencing protocol, please answer the following questions:

* What is the species you study? Any specific genomics modification?

* Please describe your sequencing platform (the consistency in platforms), coverage, sequenced region (e.g, fullgenome, exome, targeted)

* For RNAseq, is it a strand-specific library and how was the RNA captured (e.g., polyA or rRNA depletion)?

* Was it single-end, paired-end, mate-pair or a combination?

* What is/are the average insert size(s)?

* Which adapter-ligation protocol was used (TruSeq, Nextera, ...)? Please provide a list of used adaptors if possible.

* Did anyone already perform data analysis on the sequencing data (e.g., by the sequencing center)? If yes, what is the conclusion?

### If you are going to do sequencing, please answer the following questions
* Did you already find a sequencing center (e.g. LGTC, BGI) to do sequencing?

* Do you need advice on sequencing design?

### Expected deliverables:
* What kind of output datasets do you need and in which format?

* What kind of documents do you need? E.g. QC report, description of the pipelines.

* If your goal is to perform differential gene expression analysis, please specify your research question by providing which sample sets should be compared to each other. If samples are paired, please indicate in sample sheet.