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What human transcriptome annotation to use for RNA-seq analysis

Hello,

Sorry for this naive question, but I'm starting a RNAseq differential expression analysis, and it's my first time with human data.

I'm wondering which annotation should I use for my analysis, is there a "standard" annotation that is efficient and commonly used? Should I use an annotation of hg19 or hg38 assembly?

Thanks

rna-seq annotation
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updated by Benn Benn • written by guillaume.rbt guillaume.rbt

2 answers

Hi,

I would use the improved and newer one hg38

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written by caggtaagtat caggtaagtat

I use the ensembl annotation, which you can download here (Gene sets: GTF).

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written by Benn Benn

Thank for your help. As I will be using Salmon for quantification I need the sequences of all transcripts, should I get the "cDNA" Fasta for that?

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written by guillaume.rbt guillaume.rbt

Ok thanks for the information. Would it be wiser to use the "Transcript sequences", or the "Protein-coding transcript sequences" from GENCODE? (as I will be analysing expressed gene I think it's ok to use only the Protein-coding transcript sequences, but maybe I'm wrong)

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written by guillaume.rbt guillaume.rbt

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