Bulk RNA seq

Question

[B- for bioinformatics]

Hi I just started indexing with Rsubread with R packages 3.6.0. I would like to know a few things in the scripts.

library(Rsubread) 
ref <- system.file("extdata","reference.fa",package="Rsubread") 
buildindex(basename="reference_index",reference=ref)

1. What does mean about extdata means, in the script? reference.fa--- do I can download this file from https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.20/ Here in this link, I have two option in the Download Assembly

2. Source database(Genbank or RefSeq), what I have to choose from here?

3. File type, which files types, I have to select as my reference?

Answer 1

[GenoMax]

I assume you are following Rsubread vignette.

extdata refers to location where additional data installed with R packages. In this case Rsubread installs a reference file that you can find the location of by just typing ref at command prompt after you execute the second command.

If you are going to work with mouse genome then you could get the reference and annotation from GENCODE/Ensembl/NCBI. You will need a fasta reference sequence and a GTF format annotation file.