Question: (Closed) Differential Expression From The Single End Read
0
gravatar for Senthilkumar
8.3 years ago by
Senthilkumar90
Senthilkumar90 wrote:

Possible Duplicate:
Measuring differential expression using RNA-seq in organisms without a genome or transcriptome?"

I have NGS of single end read for non-model organism (control and experiemnt) done by commereical CLC bio. could anyone help me my quires. How differential expression analysis will be made. Sincee the contig of control library not match with the same contig of experimeent. any procedure or related publication for the same.

gene next-gen rna denovo sequencing • 1.9k views
ADD COMMENTlink modified 8.2 years ago by Sequer150 • written 8.3 years ago by Senthilkumar90
4

Senthil -- how's this rephrasing: I have RNA-seq data from a control and experimental condition for an organism that lacks a genome and I want to measure differential expression. I have already tried doing de novo assembly of the transcriptome separately on each sample but the contigs don't match, so I don't know how to compare them. Does anyone have any suggestions for how to assess differential expression with or without assembly of the transcriptome?

ADD REPLYlink written 8.3 years ago by Qdjm1.9k
3

Also Senthil, try changing the title of your question. Maybe: "Measuring differential expression using RNA-seq in organisms without a genome or transcriptome?"

ADD REPLYlink written 8.3 years ago by Qdjm1.9k
1

Can you rephrase this in an understandable question?

ADD REPLYlink written 8.3 years ago by Niek De Klein2.5k
0
gravatar for Sequer
8.3 years ago by
Sequer150
Malaysia
Sequer150 wrote:

You can try the Avadis NGS workflow pipeline.

ADD COMMENTlink written 8.3 years ago by Sequer150
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