I am trying to use RNA-SeQC to evaluate my RNA seq results. In its output from my pair end sequences:
Sample Note Total Purity Filtered Reads Sequenced Alternative Aligments jmp qc 10,846,940 8,148,101
Which gave me a total number of reads = 10,846,940 + 8,148,101 = 18,995,041
However, when I use command lines to count:
zcat sub592_1.fastq.gz | echo $((`wc -l`/4)) #5924954 zcat sub592_2.fastq.gz | echo $((`wc -l`/4))#5924954
which totals up to 5924954x2 = 11 849 908
The differences equals 18,995,041 - 11,849,908 = 7 145 133
Could anyone please explain what caused this discrepant result ? Thank you very much !