Salmon alignment to cancer transcriptome

Question

[zal4002]

I am trying to run a Salmon alignment of some RNASeq data from an experiment on cancer cells but the documentation uses the arabidopsis transcriptome rather than the human one. I looked on the ensembl website and found the genome but when I searched for the transcriptome I found one file related to metabolic states. Which of these is better to use or is there a better option to use for cancer in particular?

Answer 1

[ATpoint]

If it is human then quantify against the human reference transcriptome, e.g available from GENCODE:

ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.transcripts.fa.gz

Answer 2

[zal4002]

thanks! seems like that worked