Question: The Differences Of The Number Of Reads From Command Line And Rna-Seqc
gravatar for mad.cichlids
7.1 years ago by
mad.cichlids120 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 !

rnaseq quality • 1.9k views
ADD COMMENTlink modified 6.5 years ago by madk00k350 • written 7.1 years ago by mad.cichlids120

I have the same question! Did you find an answer for this?



ADD REPLYlink written 6.5 years ago by P10
gravatar for madk00k
6.5 years ago by
madk00k350 wrote:


RNAseq-QC does not count the reads that were not mapped. One can output the number of mapped reads in BAM file using samtools flagstat command or Qualimap tool. Additionaly, as I suppose, one has to exclude number of reported rRNA reads to get the number reported by RNASeq-QC.


ADD COMMENTlink written 6.5 years ago by madk00k350
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2494 users visited in the last hour