<p>To filter your gene_exp.diff either you export it to excel and then filter because it is columns separated by tabs or use the command (awk and head -n) to filter and have the number of lines you want if you master Linux</p>

CC BY-SA 4.0
2020-04-22T01:00:35.967Z
2020-04-22T01:00:35.967Z
Diango
<p><em>This question has also been asked on <a href="https://www.biostars.org/p/428956/" rel="nofollow noreferrer">Biostars</a></em></p>
<p>I have run <em><strong>cuffdiff</strong></em> (with statistics turned ON) to compare two groups of samples: <em>Control group</em> and <em>Late AD group</em>.</p>
<p>This is the command I ran to be precise:</p>
<pre><code>cuffdiff -L Control,AD_Late_Braak -p 8 --total-hits-norm --frag-bias-correct ../References/ensembl.GRCh38.99.fa --multi-read-correct --library-norm-method quartile ../References/Homo_sapiens.GRCh38.99.chr.gtf Early_Braak_Control_1,Early_Braak_Control_2,Early_Braak_Control_3 Late_Braak_Sample_1,Late_Braak_Sample_2,Late_Braak_Sample_3
</code></pre>
<p>I'm looking at the output from <em>cuffdiff</em> and I see a <em><strong>gene_exp.diff</strong></em> file which contains the results of the differential expression testing. I want to know what is the best way to filter the results of this gene_exp.diff file so as to restrict the number of genes that are up-regulated and down-regulated to a list between ~50-850.</p>
<p>P.S My thoughts are to tweak the <strong>p-values</strong> and <strong>log2 fold change</strong> values, but seems like a trail-and-error method, so I was wondering if there was a more &quot;formal&quot; method/approach?</p>

<rna-seq><differential-expression>
Filtering genes from cuffdiff results
# Filtering genes from cuffdiff results

(Asked by: username_0 on 2020-03-25)

This question has also been asked on Biostars
I have run cuffdiff (with statistics turned ON) to compare two groups of samples: Control group and Late AD group.
This is the command I ran to be precise:
cuffdiff -L Control,AD_Late_Braak -p 8 --total-hits-norm --frag-bias-correct ../References/ensembl.GRCh38.99.fa --multi-read-correct --library-norm-method quartile ../References/Homo_sapiens.GRCh38.99.chr.gtf Early_Braak_Control_1,Early_Braak_Control_2,Early_Braak_Control_3 Late_Braak_Sample_1,Late_Braak_Sample_2,Late_Braak_Sample_3

I'm looking at the output from cuffdiff and I see a gene_exp.diff file which contains the results of the differential expression testing. I want to know what is the best way to filter the results of this gene_exp.diff file so as to restrict the number of genes that are up-regulated and down-regulated to a list between ~50-850.
P.S My thoughts are to tweak the p-values and log2 fold change values, but seems like a trail-and-error method, so I was wondering if there was a more "formal" method/approach?

**Tags:** rna-seq, differential-expression

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## 1 answers

### Answer by username_1 on 2020-04-22. Score: 1

To filter your gene\_exp.diff either you export it to excel and then filter because it is columns separated by tabs or use the command (awk and head -n) to filter and have the number of lines you want if you master Linux


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