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Old 01-17-2011, 01:13 PM   #1
madsaan
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Location: california

Join Date: Jan 2011
Posts: 26
Default 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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