You have massive problems with variable scope. A "my" variable only "lives" withing the braces that surround it. Change the top of your file from 

#!user/local/perl
use Cwd;

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to this 
#!user/local/perl
use strict; use warnings; 
use Cwd;

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And then try to understand what it is telling you. If you still are confused read this Variable Scoping in Perl: the basics. If after that you don not understand how to fix it come back and show us your progress.

hint: the key will be to combine your c/d loops into a single loop. something like this 

 
  for my $c (0..$#AbsFiles){
        my $key1=undef; 
        my $key2=undef; 
        if ($AbsFiles[$c] =~ /R2_001\.fastq$/){
           open INPUT1 ... ; 
           ...stuff to set key1; 
           close INPUT1; 
           }
        if ($AbsFiles[$c] =~ /R1_001\.fastq$/$/){
           open INPUT2 ... ; 
           ...stuff to set key2; 
           close INPUT2; 
           }
        if (defined($key1) && defined($key2} && key1 eq $key2 ) { 
          ... stuff to do when both are set and equal ... 
          } 
        else { 
           ...stuff to do otherwise .. 
          } 
        } # c

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Note that i "escaped" the dot in the regexp. an escaped dot will match any character, while "\." matches a dot itself.

Note that the close does not include the lessthan/greaterthan signs, those are used to read a file, not to reference it. Also note i closed them inside the same scope i opened them, this tends to be good practice.

edit:See below Re: Running a script across multiple directories with multiple output files (problems comparing hash key values)

In reply to Re: Running a script across multiple directories with multiple output files (problems comparing hash key values) by huck
in thread Running a script across multiple directories with multiple output files (problems comparing hash key values) by msnyder424

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