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Old 03-25-2011, 11:00 AM   #1
cbil
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Default 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.
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Old 03-25-2011, 01:29 PM   #2
Jon_Keats
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0 versus 1 base index

see

http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1
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Old 03-25-2011, 02:20 PM   #3
cbil
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Thanks. The link is helpful


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