refGene.txt to gtf

[Patidar, Rajesh (NIH/NCI) [C]]

Hi,

 

I need refgene file in gtf format and I downloaded 1 from table browser along with refGene.txt

I annotated some snps against refGene.txt using annovar and was looking for the same some transcripts in the refgene.txt as well as in refgene.gtf file(I am using gtf for cufflinks). When I overlap the refgene.txt to gtf I don’t find some of the transcripts in it eg.

ALDH7A1	NM_001201377
CCT5	NM_012073
CHAT	NM_001142929
CHAT	NM_001142933
CTNND2	NM_001332
DNAH5	NM_001369
FAM105A	NM_019018
FAM105B	NM_138348
FAM173B	NM_199133
FBXL7	NM_012304

I don’t understand why I am missing these transcripts in one of the format.

 

Then I tried to convert the refGene.txt to gtf using genePredToGtf

>>./genePredToGtf file refGene.txt hg19_refGene.gtf and got following error message.

invalid unsigned integer: "-"

 

 

Could you please suggest me how to resolve this problem.

 

Thanks,

Rajesh Patidar(NIH/NCI)[C]

 

[Hiram Clawson]

Good Morning Rajesh:

You most likely have the extra bin column in his refGene.txt file.
Note the 'cut -f2' example in the usage message of genePredToGtf

This command will fetch the refGene table in gtf format:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -N \
-e "select * from refGene;" hg19 | cut -f2- | genePredToGtf file stdin refGene.gtf

See also: http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format

--Hiram