MultiRepMacsChIPSeq - combine_replicate_data

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combine_replicate_data.pl

A script to combine replicate values into a single value and written as a new data file. Replicates may be combined with a number of different methods. Replicate groups are specified with a sample file: a two-column text file with sample identifiers in the first column and its group identifier in the second. Sample identifiers must match the column name in the input replicate file. File compression is natively handled.

Usage:

combine_replicate_data.pl -i counts.txt -s samples.txt -o count_means.txt

Options:

-i --in <file>          Input file of replicate counts
-s --sample <file>      File of replicate samples and groups
-m --method <text>      Method of combining: sum mean median max
						default mean
-f --format <integer>   Number of decimals to format combined values
-o --out <file>         Output file name