Hello,
I have RNA-Sequencing data generated from Illumina HT2000 for 14 samples from the same tissue. The technician applied the same protocol for these samples except for the last sequencing step by accident.
Batch 1 (8 samples) using 50bp paired-end
Batch 2 (6 samples) using 75bp paired-end
Since I have to analyze these sample together, what is the best way to avoid batch effect or protocol difference and reviewer's criticism?
Method1: align them separately, but merge them into one matrix using RPKM/FPKM for each gene and sample
Method2: for batch2 samples, only use the first 50bp reads for alignment, ...
Method3: re-sequencing Batch1 with 75bp paired-end protocol using the library left.
Many thanks,
Shirley
I have RNA-Sequencing data generated from Illumina HT2000 for 14 samples from the same tissue. The technician applied the same protocol for these samples except for the last sequencing step by accident.
Batch 1 (8 samples) using 50bp paired-end
Batch 2 (6 samples) using 75bp paired-end
Since I have to analyze these sample together, what is the best way to avoid batch effect or protocol difference and reviewer's criticism?
Method1: align them separately, but merge them into one matrix using RPKM/FPKM for each gene and sample
Method2: for batch2 samples, only use the first 50bp reads for alignment, ...
Method3: re-sequencing Batch1 with 75bp paired-end protocol using the library left.
Many thanks,
Shirley
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