Trinity-Duplicate removal

[reema]

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.

[yueluo]

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?]

http://ivory.idyll.org/blog/trinity-in-silico-normalize.html

[What is digital normalization, anyway?]

http://ivory.idyll.org/blog/what-is-diginorm.html

[reema]

Thanks yueluo,