Trinity-Duplicate removal

reema · 02-13-2014, 08:36 AM

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 · 02-13-2014, 06:57 PM

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

reema · 02-27-2014, 02:49 AM

Thanks yueluo,

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02-13-2014, 08:36 AM	#1
reema Member Location: Scotland Join Date: Feb 2014 Posts: 27	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.

02-13-2014, 06:57 PM	#2
yueluo Member Location: Guangzhou China Join Date: Aug 2013 Posts: 82	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

02-27-2014, 02:49 AM	#3
reema Member Location: Scotland Join Date: Feb 2014 Posts: 27	Thanks yueluo,