Self Guided Transcriptome Assembly Exercise¶

I want you to develop a pipeline to do some stuff. Think about automation - e.g. what if I gave you not just 1 dataset, but 100.

Quality control the sequences
Assembly using Trinity
Run Busco

Here are some data:

https://www.dropbox.com/s/gah3q0gt3z708yu/rnaseq.1.fq.gz
https://www.dropbox.com/s/jt6bapq2kpjnoox/rnaseq.2.fq.gz

Launch an AMI and update it. For this exercise, we will use a c4.4xlarge We need to mount a hard drive of size 300Gb. There are a few different ways to do this, but I like to add the drive during the launching of the instance using the “add storage” tab. See http://angus.readthedocs.org/en/2015/MacManes_Trinity.html

Install other software: Follow directions at http://angus.readthedocs.org/en/2015/MacManes_Trinity.html

Quality Trim: See http://angus.readthedocs.org/en/2015/MacManesTrimming.html. What Quality threshold will you use?

Assemble using Trinity: See http://angus.readthedocs.org/en/2015/MacManes_Trinity.html

Run Busco: You will need to download the Arthropod reference from the BUSCO website. See http://angus.readthedocs.org/en/2015/MacManes_Trinity.html

Optional Extra Credit Exercise Do some annotation stuff like Meg showed you.

Terminate your instance¶

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