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			     PRE-ASSESSMENT
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(This pre-assessment form for the Roscoff RAD tags course 2015 is based
on a material from Software Carpentry. The original can be found at:
[http://software-carpentry.org/workshops/assess/pre-learner.html])


1 General information
=====================

  1. Name

  2. Email address

  3. What is your career stage?
     - Undergraduate
     - Graduate
     - Post-doc
     - Faculty
     - Industry
     - Support staff
     - Other:

  4. In three sentences or less, please describe your current field of
     work or research question.

  5. In three sentences or less, please describe what you expect to
     learn from this course.


2 Prior experience with high-throughput sequencing
==================================================

  1. Have you been involved in a high-throughput sequencing project
     before, or are you currently involved in one?

  2. If you have replied "Yes" to the previous question, please answer
     the following questions:
     - What was/is the project question (in one sentence)?
     - What type of high-throughput sequencing method was/is used?
     - What was/is your role in the project (experimental design,
       sequence data analysis, downstream analysis, ...)?

  3. Do you know what the FASTQ format is?

  4. Do you know what is a PHRED quality score?

  5. Given a set of raw reads in FASTQ format, would you be able to
     perform simple quality control and sequence trimming? If yes, which
     tool(s) would you use?

  6. Given a set of clean reads, would you be able to perform a de novo
     assembly into contigs? If yes, which tool(s) would you use?

  7. Given a reference sequence (e.g. genome) and clean reads, would you
     be able to map back the reads to the reference? If yes, which
     tool(s) would you use?

  8. Given an alignment of reads from different individuals, would you
     be able to identify sequence variants? If yes, which tool(s) would
     you use?

  9. Given an alignment of reads from different individuals, would you
     be able to determine individual genotypes? If yes, which tool(s)
     would you use?

  10. Given an alignment of reads from different individuals, would you
      be able to determine allele frequencies? If yes, which tool(s)
      would you use?

  11. Given a coding sequence and a list of identified variants, would
      you be able to determine which variants are synonymous and which
      are non-synonymous at the amino-acid level?


3 Informatics skills
====================

  1. What best describes how often you currently program?
     - I have never programmed.
     - I program less than one a year.
     - I program once a year.
     - I program several times a year.
     - I program once a month.
     - I program once a week or more.

  2. With which programming languages could you write a program from
     scratch that reads a column of numbers from a text file and
     calculates mean and standard deviation of that data?
     - I do not use any programming languages.
     - C
     - C++
     - Perl
     - MATLAB
     - Python
     - R
     - Java
     - Other(s):

  3. What best describes the complexity of your programming? (Choose all
     that apply.)
     - I have never programmed.
     - I write scripts that are a few lines long to analyze data.
     - I write programs that are a page or two long for my own use.
     - I write programs that are many pages long for my own use and for
       others to use.
     - I am primarily a programmer.

  4. How familiar do you think you are with the command line?
     - I am not familiar at all with the command line.
     - I am familiar only with the name "command line".
     - I am familiar with the command line but have never used it.
     - I am familiar with the command line because I have or am using
       it.

  5. Would you know how to connect to the ABiMS server from your desktop
     computer?

  6. Would you know how to upload and download data to/from the ABiMS
     server?

  7. Would you know how to submit a job on the ABiMS cluster?