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Old 05-20-2014, 02:48 AM   #1
Location: Middle East

Join Date: Apr 2013
Posts: 74
Default RNASeq Biological Replicates

Hi all,

I have RNASeq data for 20 different samples (human cell types and tissues). 10 of these samples are represented by single biological replicate, while, the other 10 samples are represented by >=2 biological replicates. In total I have 40 RNASeq fastq files mapped independently.

Now, the purpose is to compare the samples (cell types) against each other (not between the biological replicates of each sample). So, my question is: how can I deal with the biological replicates that I mapped? I have some options:

1) Take one (random) replicate per sample
2) Generate read count of mapped reads for all replicates per sample independently and then average the read counts
3) Merge the mapped reads (using bedtools merge) of the replicates

Any other suggestion?
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