14 Host transcriptomics (HT) data processing

The analysis of host transcriptomic data can be conducted following two main strategies, which depend on whether a well-annotated reference genome that contain all gene sequences of the studied transcripts is available or not. This is seldom the case in non-model organisms that lack complete reference genomes with high-quality annotation of genetic information, although many reference genome generation initiatives are rapidly increasing the number of available reference genomes. The pros and cons of using either approach have been addressed in the literature [55].

In the following two chapters, you will find example pipelines to process host transcriptomic data through both strategies:

• Reference-based host transcriptomics (HT) data processing
• Reference-free host transcriptomics (HT) data processing

References

55. Lee S-G, Na D, Park C. Comparability of reference-based and reference-free transcriptome analysis approaches at the gene expression level. BMC Bioinformatics. 2021;22 Suppl 11:310.