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Question: Do I trim paired end sets first or merge and then trim?
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gravatar for Dennis
13 months ago by
Dennis • 10
Dennis • 10 wrote:

Hi there,

I have a quick question - I have raw 10Gb -sized datasets for my samples. For each one of them I have two files from paired end reads - R1 and R2. Do I merge them first using something like fastq-join or do I process them using fastQC and then merge?

Thank you!

Best regards, Dennis
rna-seq • 1.2k views
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modified 13 months ago by Jennifer Hillman Jackson ♦ 25k • written 13 months ago by Dennis • 10
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gravatar for Jennifer Hillman Jackson
13 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

For RNA-seq analysis, QA/QC the data as distinct datasets then enter as pair-end data for differential expression analysis.

The Galaxy tutorials here cover RNA-seq processing (expression plus other analysis): https://galaxyproject.org/learn/

Another post just recently addresses paired-end data used with different tools/analysis goals. These analysis paths are covered in the tutorials.

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 13 months ago • written 13 months ago by Jennifer Hillman Jackson ♦ 25k
1

Thank you Jen!

Much appreciated!

I will read through the tutorials first. There is a lot of information - I'm just getting into RNAseq!

It is wonderful that there are public resources and help like this!

Thank you again!

ADD REPLY • link written 13 months ago by Dennis • 10
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