I set up an RNA seq experiment with 4 samples and 4 bioreplicates each. I now have a total of 16 fastq files. However, of these, 8 are going to be resequenced because number of reads were too low (though still usable). I was told that it was technical issue related to quantifying the library at the sequencing facility. When I get the new set of 8 files, how should I handle them:
1. As a completely separate technical replicate? (The same library will be used for re-sequencing)
2. Merge the BAM files together? (e.g., BR1a.BAM + BR1b.BAM)....concatenate BAMs or merge the raw reads together? (e.g.., BR1a.fastq + BR1b.fastq) concatenate fastqs?
Which of the above will give me greater statistical power. How will I make better use of the fact that I will have resequenced the same library deeper?
Thanks
Siva
1. As a completely separate technical replicate? (The same library will be used for re-sequencing)
2. Merge the BAM files together? (e.g., BR1a.BAM + BR1b.BAM)....concatenate BAMs or merge the raw reads together? (e.g.., BR1a.fastq + BR1b.fastq) concatenate fastqs?
Which of the above will give me greater statistical power. How will I make better use of the fact that I will have resequenced the same library deeper?
Thanks
Siva
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