inst/scripts/ReadMe_extdata.md

In fursham-h/factR: Functional Annotation of Custom Transcriptomes

Generating extdata

The extdata sc_merged_sample.gtf.gz contain a sample custom transcriptome constructed from cortical neural populations from a dataset by Tasic et al. (2018). To generate the full transcriptome, execute the download_assemble_sc.sh script:

bash download_assemble_sc.sh

A sample of this transcriptome was obtained by taking the first 500 genes from chromosome 15. This is done in R:

gtf <- factR::importGTF("sc_merged.gtf.gz")
chr15.genes <- unique(gtf[seqnames(gtf) == "chr15"]$gene_id)
chr15.500 <- chr15.genes[1:500]
gtf <- gtf[gtf$gene_id %in% chr15.500]
rtracklayer::export(gtf, "sc_merged_sample.gtf.gz")

fursham-h/factR documentation built on Aug. 20, 2023, 1:58 p.m.