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Old 02-13-2014, 07:36 AM   #1
reema
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Location: Scotland

Join Date: Feb 2014
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Post 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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Old 02-13-2014, 05:57 PM   #2
yueluo
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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?]
http://ivory.idyll.org/blog/trinity-...normalize.html
[What is digital normalization, anyway?]
http://ivory.idyll.org/blog/what-is-diginorm.html
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Old 02-27-2014, 01:49 AM   #3
reema
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Thanks yueluo,
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