Question about combining (technical?) replicates

Question

[collmerr]

Hello all,

I just found out that there was a problem with my last sequencing run where the robot did not load the correct sample volume into the lane. The core re-ran the samples, so now I have two files per sample: one underloaded and one correctly loaded. I'm processing the correctly loaded samples now, but I'm thinking I will probably merge the two sample files, similar to how technical replicates are handled. Do you think this is appropriate?

Thanks!

[ATpoint]

As the sequenced library is identical I would subsample to the same number of reads and then plot and calculate correlation over a defined number of regions e.g.the top 50k windows of 500bp across the genome with the highest average read count (or alternatively call peaks and use them as reference). If the Pearson cor is reasonable (for a lane replicate should probably be around .99 depending on the number of low-count regions) you can probably merge them.

Answer 1

[JC]

if there are no big bias yes, after processing just check libraries in a PCA, if there are no big differences you can merge them