Genomorientierte Bioinformatik Assignment 3

Bam Features

Sequencing in bioinformatics generates billions of reads per sample, which are aligned to the reference genome using a mapper. These data are stored in a Sequence Alignment Map (SAM) file and can be converted into a compressed format, a Binary Alignment Map (BAM) file. Various analyses can then be performed on the BAM files.

The JAR discussed in this report reads a given paired-end RNA-seq BAM file and calculates various features, which are stored in a <tsv> file. The JAR was executed on three different BAM files to compute RPKM values. Additionally, the JAR is analyzed in terms of runtime and correctness.

See Report

Usage

java -jar bam.jar 
          -bam <bamPath.bam> 
          -o <outputPath.annot> 
          -gtf <gtfPath.gtf> 
          [-frstrand <true/false>] 
          [-lengths]

Used Bam FIles

Species	BAM	GTF	frstrand
Homo Sapiens	ebna_hisat	GRCh37.75	"+"/"true"
Homo Sapiens	hes_star	GRCh37.75	"-"/"false"
Yeast	nookaew_cm	R64-1-1.75	$\times$

Read Pair Classification

Note

BioRender was used to create this figure.

Runtime

RPKM Calculation

bash rpkm.sh <sample>.annot <sample>.gene_lengths.txt

Note

sample.gene_lengths.txt is generated when calling the JAR with the -lengths flag.