Only 50% reads aligned on PE human mRNA stranded library

[cecile2429]

Hello,
We have fastq files from an Illumina stranded human mRNA library (QC ok), sequenced on novaseq X in paired end (QC ok). But when we align with salmon, we only have 50% of reads aligned. Illumina certifies that they manage to align them with their tools at 72%, but we cannot reproduce with salmon1.10.2 installed with bioconda. We used the code:
salmon quant -i human_index -l ISR -1 Fastq/R1 -2 Fastq/R2 -p 8 --validateMappings -o SALMON_OUT

If anyone can help us increase this alignment %.
Thank you for your help.
Cecile