# 2018 Transposon Insertion Sequencing Workshop

Instructor: Mark Mandel

Dates: August 13-14, 2018

## Day 1: Morning (9:30 am - 12:30 pm)

*Note: Part of Jetstream that we will use will be down starting at 10:00 am on Tuesday. Therefore, we will start right in on the hands-on portion, and tomorrow we will discuss more about the history & implementation of INSeq.*

Command line intro/refresher. [Cheat sheet](https://github.com/mandel01/programming-for-biologists/blob/master/training-resources/shell-reference.md)

[Log into the cloud (XSEDE Jetstream)](instance.html)

## Day 1: Afternoon (1:30 pm - 4:30 pm or later)

[Install the pyinseq pipeline](pyinseq.html)

[Run the data analysis pipeline](pyinseq.html#run-pyinseq)

[Download your results](download.html)

Review results

## Day 2: Morning (9:30 am - 12:30 pm)

[Historical context for INSeq](history.html)

[Considerations for experimental design](design.html)

[Transposon selection and design](transposon.html)

[Variations on the theme: alternate options to consider](variations.html)

Considerations for data deposition


## Resources

[Workshop docs rendered](http://2018-inseq-workshop.readthedocs.io)

[Workshop docs source](https://github.com/mandel01/2018-inseq-workshop)