Downloading gtf file for RefSeq

Question

[KVC_bioinfo]

Hello, I have downloaded human transcriptome (RefSeq transcripts) from this website. I want to download gene annotation file for this transcriptome. Can some one help me explaining how to do that?

I tried using ucsc table browser how ever seems like I am downloading a wrong file. Because, when I use that gtf file to count raw counts from aligned RNA-seq data (aligned to human transcriptome) I get zero for all of the transcripts.

[tarek.mohamed]

Hi,

Which genome build did you use for your alignment?

[tarek.mohamed]

you can download the annotation file from ensembl FTP

https://www.ensembl.org/info/data/ftp/index.html

[KVC_bioinfo]

I have attached the link above from where I downloaded the human transcriptome. build 38

[xiaoleiusc]

Is there a way to download the GTF for a specific gene?

[h.mon]

What exactly you downloaded, Reference Genome Sequence or RefSeq Transcripts? How did you map and count?

[KVC_bioinfo]

I used STAR aligner for mapping with human transcriptome from the link above without gene annotation file. I tried to get the total count using RseQC.

Answer 1

[h.mon]

If you are interested in transcript counts, use an appropriate tool for the task. You may map with STAR (as you did) and count with RSEM or eXpress. Even better, you could get the counts directly from an indexed transcriptome with kallisto or Salmon. These tools take into account the redundant nature of transcripts and apportion multi-mapping reads optimally using an EM algorithm.

If you are using FPKM_count.py from RSeQC, it requires a bed file, not a gtf.

Answer 2

[aka001]

You can get the refGene annotation file from the UCSC:

http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/

Just change the genome version with what you wanted.