Hi everyone,
I am looking at a 454 dataset and I am wondering whether the read sequences (they are in a FASTA file) are ususually in the same direction as the original mRNAs or can they be reverse complement?
This will determine what BLAT parameters I use during alignment. Either q=rna or q=dna. I think with standard (non-454) ESTs you don't know the orientation, so you have to use q=dna. However, this can give you unwanted duplicated alignments.
I am looking at a 454 dataset and I am wondering whether the read sequences (they are in a FASTA file) are ususually in the same direction as the original mRNAs or can they be reverse complement?
This will determine what BLAT parameters I use during alignment. Either q=rna or q=dna. I think with standard (non-454) ESTs you don't know the orientation, so you have to use q=dna. However, this can give you unwanted duplicated alignments.
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