STAR aligner : number of read

[Stéph026]

Hi,
Im' using star to map RNAseq sample in pair-end. But when I check the "..._Log.final.out" file it's mentioned for "number of input read" 17419443 read (for my sample 1).
But regarding the report of the sequencing facility i'm supposed to have 34838886 read (it mean there is exactly a fold change of 2). It's the same thing for all samples.
I try to process with one fasteQ among both (but i tried for both). And it's the same, only 17419443 read (for both).
Probably make sense when I use 1 fq, but i don't understand what happen when i use both.

Here is my code :

STAR \
--runThreadN 8 \
--outFileNamePrefix /path/sample1_ \
--genomeDir /path/genomeDir \
--outSAMtype BAM SortedByCoordinate \
--quantMode GeneCounts \
--outSAMunmapped Within \
--outSAMattributes Standard \
--readFilesIn /path/sample1_1.fq.gz /path/sample1_2.fq.gz \
--readFilesCommand zcat \

I tried to solve it by myself but I don't understand.
If someone understand what happen...

Best

Stéphane

[jdk787]

STAR counts each pair as one read.
From the manual - Note that STAR counts a paired-end read as one read,
(unlike the samtools flagstat/idxstats, which count each mate separately)