Thanks for the insightful info GenoMax. I had always thought reads were in a random order in .fastq files. Then I would also think that reads from two biological replicates where each had 3 sets of PE reads from different lanes would also have a relatively similar order.
In essence R1 and R2 are technical replicates due to bridge amplification. I am going to try and compare any differences I find in read counts using a seed in a sample and not using one. And might even compare alignment between BBMap, Hisat2, and Tophat2
In essence R1 and R2 are technical replicates due to bridge amplification. I am going to try and compare any differences I find in read counts using a seed in a sample and not using one. And might even compare alignment between BBMap, Hisat2, and Tophat2
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