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Old 07-12-2011, 05:39 AM   #1
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Location: Bs As, Argentina

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Default Creating genome compilation for cis-genome

I am new in high throughput sequencing. I'm even new using linux.

I have performe ChIP-seq experiments in tomato to map the binding sites of a transcription factor. I have been told to use the Cis-genome software to analyze the data but in the tutorial they say you have to use the available genomes on their webpage and there is no tomato genome available for that program. Does anybody know if I can actually create my own genome compilation for that program?

I only have the fasta file from the tomato chromosomes and another file with the anotated genes. I have so far build the genome using bowtie software, aligned the read withing the genome and used the IGV browser to take a look at the data.

I would appreciate any ideas or suggestions you may have
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