inst/script/README.md

In tximeta: Transcript Quantification Import with Automatic Metadata

Creation of the Salmon indices in extdata

The extdata directory contains two directories, each with a header.json file:

• Drosophila_melanogaster.BDGP6.cdna.v92_salmon_0.10.2
• Drosophila_melanogaster.BDGP6.v92_salmon_0.10.2

These directories were created by running the index step of Salmon version 0.10.2 on the Drosophila melanogaster transcriptome. The only files that have been posted are the header.json files from the index directory, as the index itself is not needed by tximeta and is too large to include. These directories allow us to demonstrate the use of tximeta when the transcriptome is not known.

The transcriptome FASTA files were downloaded from the following FTP sites:

• ftp://ftp.ensembl.org/pub/release-92/fasta/drosophila_melanogaster/cdna/Drosophila_melanogaster.BDGP6.cdna.all.fa.gz
• ftp://ftp.ensembl.org/pub/release-92/fasta/drosophila_melanogaster/ncrna/Drosophila_melanogaster.BDGP6.ncrna.fa.gz

The Drosophila_melanogaster.BDGP6.v92_salmon_0.10.2 index was created by cat-ing the cdna and ncrna gzipped FASTA together before running salmon index.

tximeta documentation built on April 13, 2021, 6:01 p.m.