Small Amounts of Replicates via Audic and Claverie Test - williamritchie/IRFinder GitHub Wiki

Similar to test without replicate, another built-in script can take a small amount of replicates (no more than 2) into account when applying Audic and Claverie test (paper).

Before calling the test, we need to pooled all replicates of the same condition together and measure that pooled IR. Unsorted.bam files can be found in the IRFinder output folder of each sample/replicate.

$ bin/IRFinder -m BAM  -r IRFINDER_REFERENCE -d pooled_WT \    
  <(samtools cat WT_replicate1/Unsorted.bam WT_replicate2/Unsorted.bam) 
$ bin/IRFinder -m BAM  -r IRFINDER_REFERENCE -d pooled_KO \    
  <(samtools cat KO_replicate1/Unsorted.bam KO_replicaet2/Unsorted.bam)

After measure the pooled IR of each condition, we can call the comparison script:

$ bin/analysisWithLowReplicates.pl \    
  -A pooled_KO/IRFinder-IR-dir.txt KO_replicate1/IRFinder-IR-dir.txt KO_replicate2/IRFinder-IR-dir.txt \    
  -B pooled_WT/IRFinder-IR-dir.txt WT_replicate1/IRFinder-IR-dir.txt WT_replicate2/IRFinder-IR-dir.txt \    
  > KO-vs-WT.txt