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madsaan 01-17-2011 01:13 PM

tophat indexing
 
Hi,

I have a couple of questions regarding the input files for tophat.I am aligning RNA-Seq reads with canfam2(dog) genome.

1.Do I have to create an index file for the RNA-seq reads like creating an index file for canfam2 genome or should I just use the fastq file directly as input.

Thanks,
Joji


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