Question: Downloading gtf file for RefSeq
1
gravatar for KVC_bioinfo
2.2 years ago by
KVC_bioinfo410
Boston
KVC_bioinfo410 wrote:

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.

rna-seq refseq gtf • 5.7k views
ADD COMMENTlink modified 2.2 years ago by h.mon28k • written 2.2 years ago by KVC_bioinfo410

Hi,

Which genome build did you use for your alignment?

ADD REPLYlink written 2.2 years ago by tarek.mohamed260

you can download the annotation file from ensembl FTP

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

ADD REPLYlink written 2.2 years ago by tarek.mohamed260

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

ADD REPLYlink written 2.2 years ago by KVC_bioinfo410

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

ADD REPLYlink written 2.2 years ago by h.mon28k

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.

ADD REPLYlink written 2.2 years ago by KVC_bioinfo410
1
gravatar for h.mon
2.2 years ago by
h.mon28k
Brazil
h.mon28k wrote:

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.

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by h.mon28k
0
gravatar for aka001
2.2 years ago by
aka001190
Sweden
aka001190 wrote:

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.

ADD COMMENTlink written 2.2 years ago by aka001190
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2111 users visited in the last hour