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Question: Downloading gtf file for RefSeq
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2.1 years ago
KVC_bioinfo • 390
Boston

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.

ADD COMMENTlink 2.1 years ago KVC_bioinfo • 390 • updated 2.1 years ago h.mon 25k
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0

Hi,

Which genome build did you use for your alignment?

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tarek.mohamed
• 250
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you can download the annotation file from ensembl FTP

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

ADD REPLYlink 2.1 years ago
tarek.mohamed
• 250
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I have attached the link above from where I downloaded the human transcriptome. build 38

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KVC_bioinfo
• 390
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What exactly you downloaded, Reference Genome Sequence or RefSeq Transcripts? How did you map and count?

ADD REPLYlink 2.1 years ago
h.mon
25k
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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.

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KVC_bioinfo
• 390
1
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2.1 years ago
h.mon 25k
Brazil

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 2.1 years ago h.mon 25k
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2.1 years ago
aka001 • 190
Sweden

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 2.1 years ago aka001 • 190

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