When running the tpmcalculator_make_matrix.pbs to create the gene and transcript level counts matrix, providing the correct tpmdir=../cohort_TPMCalculator path, the job returned an empty table.
This was due to the initialisation of the variable i=
as my $i=0; prior to the foreach for loop in both
tpmcalculator_make_matrix.pl and tpmcalculator_transcript_make_matrix.pl but being reassigned to i==1 in the for loop
my(@col)=split(" ",$_);
my $gene=$col[0];
my $tpm=$col[6];
if($i==1){
The code below resolved the issue in the tpmcalculator_make_matrix.pl script:
print "Saving gene level TPMs into memory...\n";
my $genecountshash = {};
my $i=1; # Initialising this as "my $i=1" corrected the issue
my @allgenes; my $gene; my $count;
The code below resolved the issue in the tpmcalculator_transcript_make_matrix.pl script:
print "Saving transcript level TPMs into memory...\n";
my $transcriptcountshash = {};
my $geneidhash = {};
my $i=1; # Initialising this as "my $i=1" corrected the issue
my @alltranscripts; my $gene; my $transcript; my $count;
When running the
tpmcalculator_make_matrix.pbsto create the gene and transcript level counts matrix, providing the correcttpmdir=../cohort_TPMCalculatorpath, the job returned an empty table.This was due to the initialisation of the variable
i=asmy $i=0;prior to theforeachfor loop in bothtpmcalculator_make_matrix.plandtpmcalculator_transcript_make_matrix.plbut being reassigned toi==1in the for loop my(@col)=split(" ",$_); my $gene=$col[0]; my $tpm=$col[6]; if($i==1){The code below resolved the issue in the
tpmcalculator_make_matrix.plscript:print "Saving gene level TPMs into memory...\n"; my $genecountshash = {}; my $i=1; # Initialising this as "my $i=1" corrected the issue my @allgenes; my $gene; my $count;
The code below resolved the issue in the
tpmcalculator_transcript_make_matrix.plscript:print "Saving transcript level TPMs into memory...\n"; my $transcriptcountshash = {}; my $geneidhash = {}; my $i=1; # Initialising this as "my $i=1" corrected the issue my @alltranscripts; my $gene; my $transcript; my $count;