microRNA host genes List

Question

[Soltani]

Hi biostars,

Am trying to generate file that contain all miRNA host genes (Name of host genes required), so I downloaded the mirna_context table from mirbase (The first field of that table links to the first field of the mirna table) and I read in some articles that is possible to generate this file using mysql database. Can any one help me how to do that using this tool please. Thank you in advance

Answer 1

[Siva]

Assuming that these are tab-separated text files, you can do this easily with Unix/Linux join

join -1 1 -2 1 <(sort -n -t$'\t' -k1 mirna_context.txt) <(sort -n -t$'\t' -k1 mirna.txt) > joined_file

This outputs only the lines with the same value in the first field in both files . If you also want the lines that are unique in each file, you can use the -a option.

More information about join: http://unixhelp.ed.ac.uk/CGI/man-cgi?join