This repository houses the pipeline I coded to perform differential analysis of transcriptomes from two oyster species, C. gigas and C. virginica and isolate genes in the apoptosis pathway.
Hi, Erin. I am doing transcript reconstruction and quantification using StringTie and DEA using DESeq2. I have generated the count matrices of genes and transcripts using the python script prepDE.py provided by https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual . However the gene id and transcript id are all StringTie id, how can I generate the matrices contain both StringTie id and corresponding Ensembl id? Thanks.