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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?

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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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