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Day_4

Day 4: Sequencing QC and Introduction to Read Mapping and Visualization

 

Welcome to Day 4 of the Short-Read Sequencing Analysis Workshop. After Day 4 you should have a basic understanding of how to use FastQC to evaluate the quality of your short-read data and how to trim your reads using Trimmomatic. We will also be reviewing barcoding/indexing and some of the considerations to using barcodes for multiplex sequencing. We will also cover read mapping with Bowtie2.At the end of day 4 you will have completed all the preliminary data steps for most Short read seq pipelines.

Videos

4_1_barcoding_DavidBrazel.mp4

4_2_fastQC_AmberScott.mp4

4_3_running_fastQC_DanielRamirez.mp4

4_4_trimmomatic_AmberScott.mp4

4_5_running_trimmomatic_DanielRamirez.mp4

4_6_Intro_Mapping_JessicaVera.mp4

4_7_bowtie_JessicaVera.mp4

4_8_running_bowtie2_DanielRamirez.mp4

4_9_igv_JessicaVera.mp4


Worksheets

fastqc

trimmomatic

bowtie2

Homework

day4_homework

Slides

day4_slides

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