cufflinks probem: start pos of exons

cbil · 03-25-2011, 11:00 AM

Hi , I am using Cufflinks on illumina GA data and downloaded GTF (UCSC) file from UCSC. I observed that in the gene.expr file from cufflinks output the start position of transcripts is somehow 1 base smaller than that defined in the GTF file. Do any body know why this happens? Thank you very much in advance.

Jon_Keats · 03-25-2011, 01:29 PM

0 versus 1 base index

see

http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1

cbil · 03-25-2011, 02:20 PM

Thanks. The link is helpful

Quote:

Originally Posted by Jon_Keats

0 versus 1 base index

see

http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1

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03-25-2011, 11:00 AM	#1
cbil Junior Member Location: Virginia Join Date: Mar 2011 Posts: 2	cufflinks probem: start pos of exons Hi , I am using Cufflinks on illumina GA data and downloaded GTF (UCSC) file from UCSC. I observed that in the gene.expr file from cufflinks output the start position of transcripts is somehow 1 base smaller than that defined in the GTF file. Do any body know why this happens? Thank you very much in advance.

03-25-2011, 01:29 PM	#2
Jon_Keats Senior Member Location: Phoenix, AZ Join Date: Mar 2010 Posts: 279	0 versus 1 base index see http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1