I have a script to calculate total number of occurrence of a read in fastq format in all files: 
#!/usr/bin/env perl
use strict;
use warnings;

my %compare;

$/="";
while (<>) {
chomp;
    my ( $key, $value ) = split('\t\s', $_);

   

    push( @{ $compare{$key} }, $value );

}

foreach my $key ( sort keys %compare ) {
my $tot = 0;
for my $val ( @{$compare{$key}} ) {
        $tot += $val;
    }   
    
if ( @{ $compare{$key} } >= @ARGV) {


        print join( "\t", $key, $tot, @{ $compare{$key} } ), "\n\n";
    }
}

[download]

for example I have 3 files data.txt,data1.txt,data2.txt which has the count of the occurrence of a read. The output should give the total number of occurrence in all the files as shown in output.txt. 


data.txt

@NS500278
AGATCNGAAGAGCACACGTCTGAACTCCAGTCACAACGTGATATCTCGTATGCCGTCTTCTGCTTGAAAA
+AAAAAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+GGGGGGGGGGGG
+
AAAAA#EEEEEEEEEEEEEEEE6EEEEEAEEEAE/AEEEEEEEAE<EEEEA<A/AE<EE/EEAEEAEEAE
+EEEA///EEEEEEEEEAEEEEEEEEEEEEEEEEEEEE/EEEAEEEAEEEEEEEEEAEAEEEEEEEEEEE
+EAEEEEEAEEAA     1:data.txt

@NS500278
CATTGNACCAAATGTAATCAGCTTTTTTCGTCGTCATTTTTCTTCCTTTTGCGCTCAGGCGCGGATTTGT
+TGTGATGTGGCAGCGCTCTGGCAGATTGCTACATGCGCAACATCTACCAGTTTACTTAACTGACTAAAC
+AGTAAGTCGACC
+
AAAAA#E/<EEEEEEEEEEAEEEEEEEEA/EAAEEEEEEEEEEEE/EEEE/A6<E<EEE/E6EEEEEEEE
+E6EEEE<EAEEEE<</EAEE6<<EEEEEA/AEAE<AA<E6A<E/EEE<EAEEEEAAEEE<AAE<EEEE6
+A6AEA<A6//66     3:data.txt

@NS500278
TACAGNGAGCAAACTGAAATGAAAAAGAAATTAATCAGCGGACTGTTTCTGATGTTATGGATGGCGCTGT
+TAATCGCAGCAATGGTGTATCCGCAGGGGATTTTTCCGGTACTGGCAGCGTCCGGCGTTTGGGTAGAGA
+TCGGAAGAGCAC
+
AAAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEAEEEAEEEEAEEAEEEE
+AEEEA//EEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
+EEAAAEAEEEEA     2:data.txt

[download]
data1.txt

@NS500278
AGATCNGAAGAGCACACGTCTGAACTCCAGTCACAACGTGATATCTCGTATGCCGTCTTCTGCTTGAAAA
+AAAAAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+GGGGGGGGGGGG
+
AAAAA#EEEEEEEEEEEEEEEE6EEEEEAEEEAE/AEEEEEEEAE<EEEEA<A/AE<EE/EEAEEAEEAE
+EEEA///EEEEEEEEEAEEEEEEEEEEEEEEEEEEEE/EEEAEEEAEEEEEEEEEAEAEEEEEEEEEEE
+EAEEEEEAEEAA     1:data1.txt

@NS500278
CATTGNACCAAATGTAATCAGCTTTTTTCGTCGTCATTTTTCTTCCTTTTGCGCTCAGGCGCGGATTTGT
+TGTGATGTGGCAGCGCTCTGGCAGATTGCTACATGCGCAACATCTACCAGTTTACTTAACTGACTAAAC
+AGTAAGTCGACC
+
AAAAA#E/<EEEEEEEEEEAEEEEEEEEA/EAAEEEEEEEEEEEE/EEEE/A6<E<EEE/E6EEEEEEEE
+E6EEEE<EAEEEE<</EAEE6<<EEEEEA/AEAE<AA<E6A<E/EEE<EAEEEEAAEEE<AAE<EEEE6
+A6AEA<A6//66     3:data1.txt

@NS500278
TACAGNGAGCAAACTGAAATGAAAAAGAAATTAATCAGCGGACTGTTTCTGATGTTATGGATGGCGCTGT
+TAATCGCAGCAATGGTGTATCCGCAGGGGATTTTTCCGGTACTGGCAGCGTCCGGCGTTTGGGTAGAGA
+TCGGAAGAGCAC
+
AAAAA#EEEEEEEEAEEEEEEEEEEEEEEEEEEEEAEEEEEEEE/EEEAE6AE<EAEEAEAAEEAEEEEE
+EEAE/EEAEEAEEE6EEEEEAE6A/E<EEEEEEEEAE<EEEEEA/AEEAAEEEEEE//AEE/<<<EEAE
+<66/</AE<<A6     2:data1.txt

[download]
data2.txt

@NS500278
AGATCNGAAGAGCACACGTCTGAACTCCAGTCACAACGTGATATCTCGTATGCCGTCTTCTGCTTGAAAA
+AAAAAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+GGGGGGGGGGGG
+
AAAAA#EEEEEEEEEEEEEEEE6EEEEEAEEEAE/AEEEEEEEAE<EEEEA<A/AE<EE/EEAEEAEEAE
+EEEA///EEEEEEEEEAEEEEEEEEEEEEEEEEEEEE/EEEAEEEAEEEEEEEEEAEAEEEEEEEEEEE
+EAEEEEEAEEAA     1:data2.txt

@NS500278
CATTGNACCAAATGTAATCAGCTTTTTTCGTCGTCATTTTTCTTCCTTTTGCGCTCAGGCGCGGATTTGT
+TGTGATGTGGCAGCGCTCTGGCAGATTGCTACATGCGCAACATCTACCAGTTTACTTAACTGACTAAAC
+AGTAAGTCGACC
+
AAAAA#E/<EEEEEEEEEEAEEEEEEEEA/EAAEEEEEEEEEEEE/EEEE/A6<E<EEE/E6EEEEEEEE
+E6EEEE<EAEEEE<</EAEE6<<EEEEEA/AEAE<AA<E6A<E/EEE<EAEEEEAAEEE<AAE<EEEE6
+A6AEA<A6//66     2:data2.txt

@NS500278
TACAGNGAGCAAACTGAAATGAAAAAGAAATTAATCAGCGGACTGTTTCTGATGTTATGGATGGCGCTGT
+TAATCGCAGCAATGGTGTATCCGCAGGGGATTTTTCCGGTACTGGCAGCGTCCGGCGTTTGGGTAGAGA
+TCGGAAGAGCAC
+
AAAAA#EEEEEEEEAEEEEEEEEEEEEEEEEEEEEAEEEEEEEE/EEEAE6AE<EAEEAEAAEEAEEEEE
+EEAE/EEAEEAEEE6EEEEEAE6A/E<EEEEEEEEAE<EEEEEA/AEEAAEEEEEE//AEE/<<<EEAE
+<66/</AE<<A6     2:data2.txt

[download]

output.txt

@NS500278
AGATCNGAAGAGCACACGTCTGAACTCCAGTCACAACGTGATATCTCGTATGCCGTCTTCTGCTTGAAAA
+AAAAAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+GGGGGGGGGGGG
+
AAAAA#EEEEEEEEEEEEEEEE6EEEEEAEEEAE/AEEEEEEEAE<EEEEA<A/AE<EE/EEAEEAEEAE
+EEEA///EEEEEEEEEAEEEEEEEEEEEEEEEEEEEE/EEEAEEEAEEEEEEEEEAEAEEEEEEEEEEE
+EAEEEEEAEEAA    3    1:data.txt    1:data1.txt    1:data2.txt
@NS500278
CATTGNACCAAATGTAATCAGCTTTTTTCGTCGTCATTTTTCTTCCTTTTGCGCTCAGGCGCGGATTTGT
+TGTGATGTGGCAGCGCTCTGGCAGATTGCTACATGCGCAACATCTACCAGTTTACTTAACTGACTAAAC
+AGTAAGTCGACC
+
AAAAA#E/<EEEEEEEEEEAEEEEEEEEA/EAAEEEEEEEEEEEE/EEEE/A6<E<EEE/E6EEEEEEEE
+E6EEEE<EAEEEE<</EAEE6<<EEEEEA/AEAE<AA<E6A<E/EEE<EAEEEEAAEEE<AAE<EEEE6
+A6AEA<A6//66    8    3:data.txt    3:data1.txt    2:data2.txt
@NS500278
TACAGNGAGCAAACTGAAATGAAAAAGAAATTAATCAGCGGACTGTTTCTGATGTTATGGATGGCGCTGT
+TAATCGCAGCAATGGTGTATCCGCAGGGGATTTTTCCGGTACTGGCAGCGTCCGGCGTTTGGGTAGAGA
+TCGGAAGAGCAC
+
AAAAA#EEEEEEEEAEEEEEEEEEEEEEEEEEEEEAEEEEEEEE/EEEAE6AE<EAEEAEAAEEAEEEEE
+EEAE/EEAEEAEEE6EEEEEAE6A/E<EEEEEEEEAE<EEEEEA/AEEAAEEEEEE//AEE/<<<EEAE
+<66/</AE<<A6    4    2:data1.txt    2:data2.txt
@NS500278
TACAGNGAGCAAACTGAAATGAAAAAGAAATTAATCAGCGGACTGTTTCTGATGTTATGGATGGCGCTGT
+TAATCGCAGCAATGGTGTATCCGCAGGGGATTTTTCCGGTACTGGCAGCGTCCGGCGTTTGGGTAGAGA
+TCGGAAGAGCAC
+
AAAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEAEEEAEEEEAEEAEEEE
+AEEEA//EEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
+EEAAAEAEEEEA    2    2:data.txt

[download]

In reply to count total number of occurrence in all files by umaykulsum

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