Merge duplicate samples in a table

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1

Hi

I merged 4 sequencing runs. Some samples had low reads in first three runs. These samples were repeated (with sampleids different from earlier runs) in run four. Therefore, merged table has duplicate samples. Is it possible to merge duplicate samples? Or should I retain repeat samples with higher read number and discard earlier samples with low read numbers.

Thanks.

2

Hello!

I guess you have three options:

  • As you already suggested, you can keep the sample with the highest depth
  • You can use the same sampleid in all sequencing runs and sum counts of the samples with the same id (check merging command for options)
  • Or you can group your current table to the new sample ids (check options if you want to average or sum the counts).

Best,

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