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Salmon alignment to cancer transcriptome

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?

rna-seq
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written by zal4002 • zal4002

2 answers

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

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written by ATpoint ATpoint

thanks! seems like that worked

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written by zal4002 • zal4002

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