<aside> 💡 This explains how to take a .bam file that was produced by aligning RNA-seq reads to a genome and a genome annotation file (.gtf) and

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Glossary

• BAM file: binary format of SAM files (which in turn store reads mapped to a reference genome)
• genome annotation file (.gtf): stores information where on the genome a certain feature is. Features could be genes, transcripts, … really anything! In our case, it’s coding sequences (”genes”)
• Coding sequence: DNA that encodes the protein (start codon to stop codon)
• featureCounts: a software that counts the reads aligned to a feature (coding sequence)
• reference genome: genome that the reads are mapped to

Intuition

How to do it?

Obtain your data

For the sake of this tutorial we are working with data from the thousand genome project. You can download:

• the reference genome

  AAB_6.re.fa

• the genome annotation file:

• the reads file (.fastq): ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR959/001/ERR9593591/ERR9593591.fastq.gz

Further Resources

https://hbctraining.github.io/Intro-to-rnaseq-hpc-O2/lessons/03_alignment.html