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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?]
This post can be referenced and cited at the following DOI: http://dx.doi.org/10.6084/m9.figshare.98198. For a few months, the Trinity list was...
[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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Metagenomics has improved the way researchers study microorganisms across diverse environments. Historically, studying microorganisms relied on culturing them in the lab, a method that limits the investigation of many species since most are unculturable1. Metagenomics overcomes these issues by allowing the study of microorganisms regardless of their ability to be cultured or the environments they inhabit. Over time, the field has evolved, especially with the advent...-
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