SV classification (aka SV quiz)

You can find all the files necessary to answer the questions in the folder “SV_quiz”. Within this folder you will find a subfolder corresponding to each of the questions. The tools we suggest to use are all freely available (IGV, MAFFT or LAST online) but Censor/Repbase which has a limited free use. Nonetheless, the limits of Censor should allow all of you to answer these questions. If you have any problem with Censor please ask me (Vale) or Alex 🙂

Visualise BAM files

IGV: Amazon instance or download on your computer (igvteam/igv)
To access the IGV viewer through the Amazon instance, go to Guacamole: “http://ec2-XX-XXX-XXX-XXX.compute-1.amazonaws.com:8080/guacamole/”, again replacing “XX-XXX-XXX-XXX” with your Amazon instance IP address. Go to the desktop environment and open the terminal inside of the ubuntu gui of guacamole and run this code:”./software/IGV_2.13.0/igv.sh”

If you want to do this exercise on your local computer you can download the quiz material like this:
scp [email protected]:workshop_materials/a13_structural_variation/SV_quiz/Data/SV_quiz_data.zip . replacing the “XX-XXX-XXX-XXX” with your Amazon instance IP address.

Make dotplots

MAFFT: https://mafft.cbrc.jp/alignment/server/index.html

LAST: http://lastweb.cbrc.jp

Repeat database
Censor (sequence homology to Repbase repeat database): https://www.girinst.org/censor/index.php

Q1: What is it?

Hint: Is there any signature of incongruent read mapping along the sequence of interest?

• Open the sequence and respective BAM files in IGV.

Q2: What is it?

Hint: Are there more reads piling up than expected along the sequence of interest?

• Open the sequence and respective BAM files in IGV.

Q3: What is it?

Hint: Do samples differ?

• Open the sequence and respective BAM files in IGV.

Q4: What is it?

Hint: Puff?

• Open the sequence and respective BAM files in IGV.

Q5: What is it?

Hint: Jump?

• Open the sequence and respective BAM files in IGV.
• Check the sequence with MAFFT/LAST and Censor.

Q6: What is it?

Hint: What happens in sample2 with respect to the reference and sample1?

• Open the sequence and respective BAM files in IGV.
• Check the sequence with MAFFT/LASTZ and Censor.

Q7: What is it?

Hint: Another jump?

• Open the sequence and respective BAM files in IGV.
• Check the sequence with MAFFT/LASTZ and Censor.

Answers

Hint: There is only one answer per sequence.