1st lab Workshop: A Beginner's Guide to NGS Data Analysis (24-25 May 2017)

kacst-bioinfo-lab / labwork

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Closed MManee closed 7 years ago

MManee commented 7 years ago

We need to do the following:

Prepare your slides
Prepare tutorials to help you delivering your presentation effectively
Prepare your pipeline
- We need to list tools we will use in all pipelines including links to download page and installation instructions
Prepare sample data to be used as a raw data
Run pipelines and make sure they are working properly with no errors and within the time allowed

amer1404 commented 7 years ago

introduction to linux session

SULTAN-ALHARBI commented 7 years ago

Working with MacTerminal:

Checking Quality of RNA-seq Datasets using fastqc https://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc
```
$./fastqc fastqfiles
$./fastqc read_1.fastq, read_2.fastq
```
Indexing your reference genome fasta file using bowtie2-build https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.2/bowtie2-2.3.2-legacy-macos-x86_64.zip/download
```
$./bowtie2-build [options]* <reference_in> <bt2_base>
$./bowtie2-build -f lambda_virus.fa lambda_virus
```