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Old 04-12-2013, 12:22 AM   #1
oxydeepu
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Location: bangalore,india

Join Date: Jul 2011
Posts: 41
Default Visualing the alignment on a genome without annotations

Hi All,

I'm working in a lab which uses planaria as a model organism, which have a contig level of genome assembly. I have RNA-Seq data from the same. Now I am trying to visualize the alignment of the reads on the genome. I also want to visualize the transcripts made from the cufflinks assembly of those RNA-Seq reads. The problem is RNA-Seq alignment is using bowtie and Cufflinks transcripts are using blast. Can anyone help me in visualizing the same. I just want to validate that the transcripts alignment on the genome corresponds to the RNA-Seq alignment. Please help. Thank you in advance.

Best Regards,
Deepak
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