Question: refseq transcriptome annotation
0
gravatar for Joe.waldron
9 weeks ago by
Joe.waldron0 wrote:

I have some next generation sequencing data that I am planning to map to the refseq transcriptome. However, the FASTA file that I have dowloaded doesn't have the positions of the UTRs/CDSs unlike the GENCODE FASTA which does have this information. I have been struggling to find the annotation for these transcripts on the refseq website. Can anyone point me in the right direction? Many thanks

sequencing rna-seq assembly • 215 views
ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by Joe.waldron0
1

RefSeq is not a genome annotation system to start with, it's a collection of sequences that are annotated/linked to other NCBI resources. I would suggest using an annotated reference genome resource such as provided by Ensembl (which includes the GENCODE data).

ADD REPLYlink written 9 weeks ago by Jean-Karim Heriche13k

OK Thanks very much for your reply

ADD REPLYlink written 9 weeks ago by Joe.waldron0

Why don't you just use GENCODE?

ADD REPLYlink written 9 weeks ago by Emily_Ensembl13k

We're particularly interested in 5'UTRs and I've read that the annotation of 5' ends is better in refseq

ADD REPLYlink written 9 weeks ago by Joe.waldron0

Which organism are we talking about?

ADD REPLYlink written 9 weeks ago by Macspider1.6k

humans

ADD REPLYlink written 9 weeks ago by Joe.waldron0

GTF files from all (REFSEQ, GENCODE, UCSC) have CDS information. Why not use GTF file to extract UTRs?

ADD REPLYlink written 9 weeks ago by Satyajeet Khare1.1k
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