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

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.

hg19 bed format conversion gtf

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updated 12.2 years ago by Kamil

• written 13.0 years ago by newDNASeqer

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

• 143 views • link

written 13.0 years ago by Chris Miller

2 answers

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

• 124 views • link

written 13.0 years ago by Ashutosh Pandey

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/

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updated 6.6 years ago by Ram

• written 12.2 years ago by Kamil

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