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Full Discussion: Comparing and merging two text files
Top Forums UNIX for Dummies Questions & Answers Comparing and merging two text files Post 302799911 by ant55 on Sunday 28th of April 2013 07:48:12 AM
Old 04-28-2013
Comparing and merging two text files
Hey everybody,

I am new here and already a question to ask, I just recently started some bioinformatic work for my PhD so I am slowly learning

Anyway, here is my problem, I have two text files, one contains the complete data file with 43000 genes and their read counts for all my samples (actually 13 columns in total):

Code:
Ant-TAContig10	2025	1276	731	308	237	63	296	
Ant-TAContig100	5340	1711	7322	1088	5018	757	2788	
Ant-TAContig1000	1101	428	650	164	358	67	301	
Ant-TAContig10000	3585	1882	2621	532	838	216

And the other text file is a list of the 21000 genes which have high expression value that I want to extract

Code:
Ant-TAContig10
Ant-TAContig100
Ant-TAContig1000
Ant-TAContig10000
Ant-TAContig10003
Ant-TAContig10005
Ant-TAContig10006

Okay so all I want to do is extract the genes in file 2 from the file 1 so I get expression value of only these 21000 genes

I sorted the files and tried join
Code:
join file1 file2 > out.txt

But the outfile is empty

I tried comm and diff but nothing seems to work

Any ideas why it does not work and hints for me please?

Thanks again everybody, have a nice sunday
Last edited by Scrutinizer; 04-28-2013 at 01:37 PM.. Reason: code tags
 

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