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I don't have a direct answer to this, but I think the following links might help you understand what the "In-silico-normalization" is doing :
[What does Trinity's In Silico normalization do?]
[What is digital normalization, anyway?]
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Trinity-Duplicate removal
Dear All,
I am using trinity for transcriptomics assembly. I have few queries:-
1) have two condition(Control and Treated) and each condition has 4 replicates. so if I merge these .fq files together, how the generated assembly from this merged .fq file would be better than the assembly generated from single(using only one replicate) sample?
2) Do I need to remove duplicates from individual fastq file before merging or after merging them together?
3) I saw there is a script "fasta_remove_duplicates" in the trinity folder. So is there any chance that "In-silico-normalization" in trinity take care of these duplicate reads?
I would appreciate any explanations.
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