Merge counts data of run-feature

To merge the TPM value generated by run-featurecounts.R, run the following code:

1. Data format

head Leaf.count 
gene_id        counts   fpkm                tpm
LOC_Os01g01010  110 0.945530723017136   2.29771048604873
LOC_Os01g01019  1   0.0231100918830517  0.0561592544383935
LOC_Os01g01030  4   0.0422809635587651  0.102745908688424
LOC_Os01g01040  49  0.480138677222636   1.16677295254003
LOC_Os01g01050  33  0.421523995695231   1.02433488563918
LOC_Os01g01060  37  1.04746491459932    2.54541820742018
LOC_Os01g01070  24  0.330032611009917   0.80200396729127
LOC_Os01g01080  82  1.03523801807094    2.51570593294702
LOC_Os01g01090  0   0   0

2. Script

#usr/bin/perl -w
 use strict;

my ($sample_list)=@ARGV;
my @sample_list=split (",",$sample_list); # list the input file in "," sperated

#print "@sample_list\n";

my %read_count;
foreach my $sample(@sample_list)
{
    open SAMPLE, $sample or die "$!";
    
    while (my $line=<SAMPLE>)
    {
        chomp $line;
            my($gene_id,$count,$fpkm,$tpm)=split("\t",$line);
                push @{$read_count{$gene_id}},$tpm;
                                    }
   }

print "gene_id\t",join ("\t",@sample_list),"\n";
foreach (keys %read_count)
    {
      my @count =@{$read_count{$_}};
          print "$_\t",join("\t",@count),"\n";
        }

Run the code:

 perl merge_reads_counts.pl  Leaf.count,sperm.count,whole_root.count |head
# Leaf.count,sperm.count,whole_root.count were seperated by ,

Results:

gene_id          Leaf.count            sperm.count          whole_root.count
LOC_Os02g54490   0.0537507259040929   0.31463009388691      0.591264432584185
LOC_Os08g24870   0.010532780787497    0                     0
LOC_Os05g16040   0                    0                     0
LOC_Os12g29280   0                    0                     0.459882614309195
LOC_Os11g36090   0.0186041974579863   0                     0.0170540336411885
LOC_Os07g43800   0                    0.44899492265031      19.8109637625006
LOC_Os02g15390   0                    0                     0.125988756671712
LOC_Os09g21140   0                    0                     0
LOC_Os02g11060   0.341296176014754    0.69763695815633      2.6766760505955

验证

grep LOC_Os02g54490 whole_root.count|awk '{print $4}'
0.591264432584185
grep LOC_Os02g54490 sperm.count|awk '{print $4}'
0.31463009388691
grep LOC_Os02g54490 Leaf.count|awk '{print $4}'
0.0537507259040929
......................................................................................
grep LOC_Os11g36090  Leaf.count|awk '{print $4}'
0.0186041974579863
grep LOC_Os11g36090  sperm.count|awk '{print $4}'
0
grep LOC_Os11g36090  whole_root.count|awk '{print $4}'
0.0170540336411885