Question: Splitting the overall RNA-seq data
1
gravatar for aeserrano
22 months ago by
aeserrano40
aeserrano40 wrote:

Hi. I am newby at bioinformatics. I have done an experiment: three replicates of Control, three replicates of Treatment 1 and three replicates of Treatment 2. I had a service provider do RNA-seq with some bioinformatic analysis. What I received was an overall analysis even if I had told the service provider that this was actually two experiments with a common control. Now, how do I separate the analyses between Control and Treatment 1 AND Control and Treatment 2? Will I do again de novo assembly for each? I suspect that separating them in terms of DEGs is a lot easier. What about annotation?

rna-seq • 638 views
ADD COMMENTlink written 22 months ago by aeserrano40
1

What I received was an overall analysis even if I had told the service provider that this was actually two experiments with a common control. Now, how do I separate the analyses between Control and Treatment 1 AND Control and Treatment 2?

It's unclear which data you got from your service provider.

Will I do again de novo assembly for each?

This suggests that you don't have a reference genome, although you didn't tell us anything about that.

ADD REPLYlink written 22 months ago by WouterDeCoster38k
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What kind of files do you have currently? What do you mean by overall analysis? If you have the raw count of each gene in each condition you can maybe redo an analysis to get DEGs between the conditions that you want.

ADD REPLYlink written 22 months ago by guillaume.rbt540
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What I mean by overall analysis is treating the 9 libraries as one experiment. What I have planned and explained to the service provider was to consider these as 2 expts with a COMMON control but still they they processed it as if it were one experiment.

ADD REPLYlink written 22 months ago by aeserrano40
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What kind of files do you have currently?

If you want help it would be best if you answer our questions.

ADD REPLYlink written 22 months ago by WouterDeCoster38k
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I have clean reads as well as raw reads

ADD REPLYlink written 22 months ago by aeserrano40
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I have clean reads as well as raw reads

ADD REPLYlink written 22 months ago by aeserrano40
1

With reads you would have to map them against your reference genome to get alignment (bam) files, and then count your reads and perform differential expression between the conditions you're interested in. But it would be easier for you to ask your provider directly for normalized read count, then perform differential expression analysis on this.

ADD REPLYlink written 22 months ago by guillaume.rbt540
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