Question: What human transcriptome annotation to use for RNA-seq analysis
0
gravatar for guillaume.rbt
10 months ago by
guillaume.rbt770
France
guillaume.rbt770 wrote:

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 • 284 views
ADD COMMENTlink modified 10 months ago by Benn7.9k • written 10 months ago by guillaume.rbt770
1
gravatar for caggtaagtat
10 months ago by
caggtaagtat930
caggtaagtat930 wrote:

Hi,

I would use the improved and newer one hg38

ADD COMMENTlink written 10 months ago by caggtaagtat930
1
gravatar for Benn
10 months ago by
Benn7.9k
Netherlands
Benn7.9k wrote:

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

ADD COMMENTlink modified 10 months ago • written 10 months ago by Benn7.9k

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?

ADD REPLYlink modified 10 months ago • written 10 months ago by guillaume.rbt770
4

You could do that.

Alternatively, GTF files and fasta files for transcripts are also available from GENCODE site (where Ensembl data comes from).

ADD REPLYlink modified 10 months ago • written 10 months ago by genomax78k

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)

ADD REPLYlink written 10 months ago by guillaume.rbt770
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