text: user4845: I have two types of files for a gene in a folder
  File 1: FOS.tf.txt 
  ABL2
  ACTN4
  ADGRE5
  ADIPOR2
  ADRB2
  ERCC4
  EZR
  FAS
  FMO4
  
  File 2: FOS.tt.txt
  ABL2
  CASP9
  CCK
  DDIT3
  ERCC4
  EZR
  FAS
  FMO4
  
  After running command 
  join FOS.tf.txt FOS.tt.txt > FOS_final.txt
  
  I got output file: FOS_final.txt
  ABL2
  ERCC4
  EZR
  FAS
  FMO4
  
  My question is that I have these two type of files (tf and tt) for 605 genes in a folder and I want to run join command together for all my genes and get 605 output files.
  
  user96: If all of your .tf.txt and .tt.txt files are in the same directory, the following command should work.
  for tffile in $(ls *.tf.txt)
  do
      prefix=$(basename $tffile .tf.txt)
      join ${prefix}.tf.txt ${prefix}.tt.txt > ${prefix}_final.txt
  done
  
  
original_text: 4845: <p>I have two types of files for a gene in a folder</p>
  
  <p>File 1: FOS.tf.txt </p>
  
  <pre><code>ABL2
  ACTN4
  ADGRE5
  ADIPOR2
  ADRB2
  ERCC4
  EZR
  FAS
  FMO4
  </code></pre>
  
  <p>File 2: FOS.tt.txt</p>
  
  <pre><code>ABL2
  CASP9
  CCK
  DDIT3
  ERCC4
  EZR
  FAS
  FMO4
  </code></pre>
  
  <p>After running command </p>
  
  <pre><code>join FOS.tf.txt FOS.tt.txt &gt; FOS_final.txt
  </code></pre>
  
  <p>I got output file: FOS_final.txt</p>
  
  <pre><code>ABL2
  ERCC4
  EZR
  FAS
  FMO4
  </code></pre>
  
  <p>My question is that I have these two type of files (tf and tt) for 605 genes in a folder and I want to run join command together for all my genes and get 605 output files.</p>
   96: <p>If all of your <code>.tf.txt</code> and <code>.tt.txt</code> files are in the same directory, the following command should work.</p>
  
  <pre><code>for tffile in $(ls *.tf.txt)
  do
      prefix=$(basename $tffile .tf.txt)
      join ${prefix}.tf.txt ${prefix}.tt.txt &gt; ${prefix}_final.txt
  done
  </code></pre>
  