How To Convert Hg19_Known_Gene From Text Format To Gtf Or Bed?

Question

[newDNASeqer]

I downloaded hg19_knownGene.txt from annovar database, and want to convert it to gtf or bed format. I have tried to google the solution and found that UCSC offered a tool called predToGtf that can do this. However, this tool does not run on my mac. I wonder if there's any alternative.

[Chris Miller]

It would help if you could edit your question to include a few lines of the file that you want to convert.

Answer 1

[Ashutosh Pandey]

You can download the knownGene data for hg19 from ucsc genome browser in a gtf format itself. Select GTF file as a output format.

try this link: hg19_ucsc _knownGenes_gtf

Answer 2

[Kamil]

See the answer to a related question: A: Obtaining Ucsc Tables Via Ftp And Converting Them To Proper Gff3 Via Genepredtog

Since you use a Mac, you'll likely want to get the executable here: http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/