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Old 03-19-2013, 08:53 AM   #1
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Location: India

Join Date: Mar 2013
Posts: 9
Default how to run tophat without gtf file and annotate the gene

Hi everyone..
i m working on RNA seq data. i dont have ref genome for my RNA seq data. i have CDS as reference genome file for my referenced. i want to run tophat on the same. how can i run tophat without gtf/gff file. after mapping with tophat how i annonate my gene/transcript covered in mapping and differentially expressed in cuffdiff pipeline. how can i annotate it without reference gtf file ?? can someone help me? Any suggestions are Appreciate. Thanks in advance.
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