Hi

Currently I have pair-end mouse RNA-seq data. 3 Tissues with 17 samples/tissue. Length of the sequence is from 100bp to 150bp. My goal is to perform DEG after the alignment. This is my first time to use STAR for alignment. I have carefully went through the STAR manual. Besides the basic parameters, I notice there are a lot of more advanced options to do in STAR. So I wonder, in practice, which parameters should I also consider to use? Below is my own set up.

Step 1:

                       STAR --runThreadN 12 \
                                 --runMode genomeGenerate \
                                 --genomeDir genomedir \
                                 --genomeFastaFiles ./ref/GRCm39.primary_assembly.genome.fa \
                                 --sjdbGTFfile ./ref/gencode.vM27.primary_assembly.annotation.gtf \
                                 --sjdbOverhang 100

Step 2:

                       STAR --runThreadN 12 \
                                 --runMode alignReads \
                                 --twopassMode None \
                                 --genomeDir genomedir \
                                 --sjdbGTFfile ref/gencode.vM27.primary_assembly.annotation.gtf \
                                 --sjdbOverhang 100 \
                                 --readFilesIn "R1_001_trim.fastq.gz" "R2_001_trim.fastq.gz" \
                                 --readFilesCommand zcat \
                                 --outFileNamePrefix "./align_output/try1_" \
                                 --outSAMtype BAM SortedByCoordinate \

Which other parameters do you think I should use? may be set "twopassMode" to "basic"? I saw mamy people doing that. Thanks in advance!