Question: The Differences Of The Number Of Reads From Command Line And Rna-Seqc
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mad.cichlids • 120 wrote:
Hi, all
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 !
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modified 6.5 years ago
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madk00k • 350
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7.1 years ago by
mad.cichlids • 120
I have the same question! Did you find an answer for this?
~Rini