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Testing different capture reaction template
I did a test of capture sequencing :
96 libraries representing 56 individuals
For one individual we made 1,2,3 or 4 libraries.
The libraries were pooled before capture reactions so that the same individual (not the same library) can be found in different capture reactions.
In total we made 6 capture reactions with different conditions (level of multiplexing or dilution)
The Sequencing was done on a NextSeq,on one flowcell with 4 lanes.
I want to evaluate the effect of the different conditions of the capture reactions on my capacity to call good quality variant.
I have 96 (f and r) fastq files : all reads in a fastq file are from the same library and the same run but are from different lanes.
I have read your documentation and I was wondering if I should split my dataset depending on the capture condition and then follow the good practices for each condition or in some way include the capture condition in the "READ_GROUP_NAME" of the uBAM file ?