Any difference between refGene and refFlat when obtaining a GTF file using the genePredToGtf tool

[Yung-Chih Lai]

Hi,

 

Using the human hg19 as an example, I want to get a GTF  file for RNA-Seq quantification (htseq-count). I used two command lines below, are they the same? I don’t see any difference between the two GTF files I downloaded. However, if they are the same, why UCSC keep both of them? Many thanks.

 

> genePredToGtf hg19 refGene hg19refGene.gtf

> genePredToGtf hg19 refFlat hg19refFlat.gtf

 

Best,

 

Gary

[Luvina Guruvadoo]

Hello Gary,

Thank you for your question. The refGene and refFlat tables are both in genePred format. However, refGene contains additional info. Please see the following links for a description of each table:

refGene:
http://genome.ucsc.edu/cgi-bin/hgTables?hgta_doSchemaDb=hg38&hgta_doSchemaTable=refGene

refFlat:
http://genome.ucsc.edu/cgi-bin/hgTables?hgta_doSchemaDb=hg38&hgta_doSchemaTable=refFlat

Note, you can view the description for any table by clicking the "describe table schema" button on the Table Browser.

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Regards,

Luvina

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Luvina Guruvadoo
UCSC Genome Browser
http://genome.ucsc.edu

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