#C0493FQQZ3P Hi, I’m currently working with the nf-core rnasplice module and have a question about paramters used to build reference

--aligner star

and

--save_reference

options using

GENCODE

genome in the pipeline. As this is short read RNA-Seq splicing analysis with 150 bp, I was wondering if

--sjdboverhang 150

parameter was used to build this reference. NOTE;

--sjdboverhang

in the STAR specifies the length of the genomic sequence around the annotated junction to be used in constructing the splice junctions database (in my case the PE read length is 150 bp)

nextflow run /projects/toufim/nfcore_rnasplice/1_0_4/rnasplice \
--input /flashscratch/toufim/23_Palucka_003_004_samplesheet.csv \
--contrasts /flashscratch/toufim/23_Palucka_003_004_Contrastsheet.csv \
--outdir /flashscratch/toufim/ \
--fasta /projects/toufim/GENCODE/GRCh38.p14_Release_47/GRCh38.primary_assembly.genome.fa \
--gtf /projects/toufim/GENCODE/GRCh38.p14_Release_47/gencode.v47.primary_assembly.annotation.gtf \
--aligner star \
--save_reference \
--gencode \
--rmats_paired_stats true \
--rmats_read_len 150 \
--sashimi_plot false \
--dexseq_dtu false \
-profile test \
-c /flashscratch/singularity_cache_nfcore/test.config \
-resume

Additionally, I don’t see

--sjdboverhang 150

used in the /genome/index/star/Log.out file?

##### Finished reading parameters from all sources

##### Final user re-defined parameters-----------------:
runMode                           genomeGenerate
runThreadN                        12
genomeDir                         star/
genomeFastaFiles                  GRCh38.primary_assembly.genome.fa
genomeSAindexNbases               14
limitGenomeGenerateRAM            64324509440
sjdbGTFfile                       gencode.v47.primary_assembly.annotation.gtf

-------------------------------
##### Final effective command line:
STAR   --runMode genomeGenerate      --runThreadN 12   --genomeDir star/   --genomeFastaFiles GRCh38.primary_assembly.genome.fa      --genomeSAindexNbases 14   --limitGenomeGenerateRAM 64324509440   --sjdbGTFfile gencode.v47.primary_assembly.annotation.gtf
----------------------------------------

In this scenario shall I use pre-built STAR index with

--sjdboverhang 150

?