Integrative Comparison of Burrows-Wheeler Transform-Based Mapping Algorithm with de Bruijn Graph for Identification of Lung/Liver Cancer-Specific Gene.

ABSTRACT: Cancers of the lung and liver are the top 10 leading causes of cancer death worldwide. Thus, it is essential to identify the genes specifically expressed in these two cancer types to develop new therapeutics. Although many messenger RNA (mRNA) sequencing data related to these cancer cells are available due to the advancement of next-generation sequencing (NGS) technologies, optimized data processing methods need to be developed to identify the novel cancer-specific genes. Here, we conducted an analytical comparison between Bowtie2, a Burrows-Wheeler transform-based alignment tool, and Kallisto, which adopts pseudo alignment based on a transcriptome de Bruijn graph using mRNA sequencing data on normal cells and lung/liver cancer tissues. Before using cancer data, simulated mRNA sequencing r

SUBMITTER: Ajaykumar A 

PROVIDER: S-EPMC9628837 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature