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Old 10-22-2010, 06:33 AM   #1
Shruti Madhiwalla
Junior Member
Location: MA

Join Date: Sep 2010
Posts: 4
Default RNA Seq alignment?

This is the first time I am dealing with RNA Seq data (Illumina, GEO data) I wish to align it to the ref genome and was thinking of using Genome Quest. Has anyone tried this software? While preparing the reads, it ask if the format of sequence is Fastaq phred quality, FastaQv1.2 or FastaQv1.3, I am not sure which to choose or how to find out what format is your sequence.

If anyone can suggest a workflow that would be helpful.

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