Question: refseq transcriptome annotation
0
gravatar for Joe.waldron
11 days 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 • 155 views
ADD COMMENTlink modified 11 days ago • written 11 days 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 11 days ago by Jean-Karim Heriche13k

OK Thanks very much for your reply

ADD REPLYlink written 10 days ago by Joe.waldron0

Why don't you just use GENCODE?

ADD REPLYlink written 11 days 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 11 days ago by Joe.waldron0

Which organism are we talking about?

ADD REPLYlink written 11 days ago by Macspider1.5k

humans

ADD REPLYlink written 11 days 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 days ago by Satyajeet Khare1.0k
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