convert gtf -> ucsc gene track format

dietmar13 · 04-08-2013, 07:33 AM

hello,

does anybody know a script to convert a gtf-file to the ucsc gene track files needed for RUM index generation.

alex (dobin): why is gencode UCSC FAs (chr1, chr2, ...) based???

I need a file in the following format (like downloading a track from ucsc):
- name (ENST000000001)
- chrom (chr1, chr2, ...)
- strand (-,+)
- exonStarts (zero-based: xxx,yyy,zzz,)
- exonEnds (one-based: aaa,bbb,ccc,)

I want make an index for RUM using Gencode 15 annotation,
but unfortunately Gencode is UCSC HG19-FA based.

for generating an index for RUM you need either ENSEMBL FAs (1,2,...) and the corresponding GTF files

or

UCSC HG19 FAs (chr1, chr2, ...) and UCSC gene tracks (name, chrom, strand, exonStarts (zero based), exonEnds (one based))

thank you,

dietmar

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
how to convert UCSC gene names to gene symbol	gigigou	Bioinformatics	5	05-19-2015 05:23 AM
GTF file from UCSC with Gene name???	golharam	General	2	09-17-2012 12:28 PM
UCSC GFF track	Palgrave	Bioinformatics	0	03-06-2012 08:13 AM
tophat -G gene model annotations GTF format?	silin284	Bioinformatics	15	04-21-2011 07:26 AM
UCSC genes in GTF/GFF format	bogdan	Bioinformatics	1	11-20-2010 09:39 PM

04-08-2013, 07:33 AM	#1
dietmar13 Senior Member Location: Vienna Join Date: Mar 2010 Posts: 107	convert gtf -> ucsc gene track format hello, does anybody know a script to convert a gtf-file to the ucsc gene track files needed for RUM index generation. alex (dobin): why is gencode UCSC FAs (chr1, chr2, ...) based??? I need a file in the following format (like downloading a track from ucsc): - name (ENST000000001) - chrom (chr1, chr2, ...) - strand (-,+) - exonStarts (zero-based: xxx,yyy,zzz,) - exonEnds (one-based: aaa,bbb,ccc,) I want make an index for RUM using Gencode 15 annotation, but unfortunately Gencode is UCSC HG19-FA based. for generating an index for RUM you need either ENSEMBL FAs (1,2,...) and the corresponding GTF files or UCSC HG19 FAs (chr1, chr2, ...) and UCSC gene tracks (name, chrom, strand, exonStarts (zero based), exonEnds (one based)) thank you, dietmar