Hi #CE8SSJV3N, I am currently running the nf-core/rnaseq-3.20.0pipeline with the

star_rsem

aligner-quantification method. My data consists of 6 Illumina short-read RNA-Seq (150 bp paired-end - reverse stranded), and my goal is to perform differential gene expression analysis between 2 groups. The job finished successfully. When I review the multiQC report, I don’t find the summary statistics from the STAR alignment and Alignment Scores as compared to when I run another case using the

--aligner star_salmon

. Additionally, I see the samtools metrics also differ between the 2 runs (

star_rsem

vs

star_salmon

). I am attaching the alignment metrics for reference. Any thoughts about this? Code:

nextflow run /projects/lab/toufim/nfcore_rnaseq/pipelines/rnaseq-3.20.0 \
--input/projects/lab/sample_info.csv \
--outdir /projects/lab/RNAseq/ \
--star_index /projects/lab/STAR_Index_GENCODE/GRCh38.p14_release_48/ref_index/ \
--fasta /projects/lab/STAR_Index_GENCODE/GRCh38.p14_release_48/hg38.fa \
--gtf /projects/lab/STAR_Index_GENCODE/GRCh38.p14_release_48/gencode.v48.annotation.gtf \
--aligner star_rsem \
--gencode true \
--gtf_extra_attributes gene_id \
--igenomes_ignore \
-c /projects/lab/toufim/singularity_cache_nfcore/mod.config \
-resume

Thank you, Toufiq