🧬 Quantify hERV and transgenes from Bulk-RNAseq
Human Endogenous Retroviruses (hERVs) are ancient viral sequences embedded in the human genome. Transgenes are common in transgenic mouse models. To quantify them from sequencing reads, we need-- a) modify fasta and gtf files to include the their sequencing and annotation; b) a feature quantification algorithm to handle multimapping commonly seen for hERV and transgenes. Here I discussed the algorithms for feature quantification, and successfully quantified hERV and transgenes by implementing an EM algorithm.
May 27, 2025
🧬 A snakemake pipline-- quantify hERV, transgenes and genomics from well-based single-cell RNAseq
Well based scRNAseq has many more details than 10x scRNAseq to pay attention to in order to quantify features using Starsolo. Here, we discuss and present the snakemake pipline to quantify hERV, transgenes and genomics from well-based single-cell RNAseq data
May 27, 2025
🧬 A snakemake pipline-- quantify hERV, transgenes and genomics from 10x scRNAseq
A snakemake pipline to quantify hERV, transgenes and genomics from 10x single-cell RNAseq data
May 27, 2025