This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Fast QC results (per sequence GC content) - RNA seq

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?

enter image description here

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?

enter image description here

fastqc rna-seq
• 1,236 views • link
written by comu • comu

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.

• 0 views • link
written by Trivas • Trivas 
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 :)

• 0 views • link
updated by GenoMax GenoMax • written by comu • comu

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.
• 0 views • link
written by GenoMax GenoMax

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

• 0 views • link
written by Ram Ram

0 answers

No answers yet.

Log in to answer this question.

More posts like this