Fast QC results (per sequence GC content) - RNA seq

Question

[comu]

Please help me to understand what is these two peaks(1st peak 37%, 2nd peak 50%)..

This result is data downloaded from an RNA seq in another experiment. Is it because it was before trimming, or is it because of the adapter? Is it possible to troubleshoot only if QC is performed after STAR is performed?

Additionally, in the mapping results, the number of input reads was 51964207, but in featurecounts of the same data, the total alignments were 108149668, which was almost double. What could be the cause?

[Trivas]

Can you post the command you used to run featurecounts? It looks like you have paired end reads but are mapping in single-end mode.

[comu]

featureCounts -T 16 -p -a /media/nutrigenomics505/505_RNA/HMCH/chhm/CHK_STAR/AnnotationFile_GTF/gencode.vM33.annotation.gtf -o /media/nutrigenomics505/505_RNA/HMCH/chhm/CHK_STAR/STAR_final_output/SRR9971982.txt /media/nutrigenomics505/505_RNA/HMCH/chhm/CHK_STAR/STAR_output/SRR9971982Aligned.sortedByCoord.out.bam

This is my command! I apply "-p", because it is paired-end...Is it wrong? Thank you for your comment :)

[GenoMax]

With newer versions of featureCounts you need to explicitly add following in addition to -p.

--countReadPairs    If specified, fragments (or templates) will be counted
                      instead of reads. This option is only applicable for
                      paired-end reads. For single-end data, it is ignored.

[Ram]

What is "Rinux"? Is it a specific flavor of linux?