Question: What human transcriptome annotation to use for RNA-seq analysis
0
gravatar for guillaume.rbt
12 days ago by
guillaume.rbt540
France
guillaume.rbt540 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 • 109 views
ADD COMMENTlink modified 12 days ago by Benn6.6k • written 12 days ago by guillaume.rbt540
1
gravatar for caggtaagtat
12 days ago by
caggtaagtat500
caggtaagtat500 wrote:

Hi,

I would use the improved and newer one hg38

ADD COMMENTlink written 12 days ago by caggtaagtat500
1
gravatar for Benn
12 days ago by
Benn6.6k
Netherlands
Benn6.6k wrote:

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

ADD COMMENTlink modified 12 days ago • written 12 days ago by Benn6.6k

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 12 days ago • written 12 days ago by guillaume.rbt540
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 12 days ago • written 12 days ago by genomax65k

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 12 days ago by guillaume.rbt540
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