Using STAR for mouse RNA-seq alignment, which parameters of STAR besides the basic ones would be better to use in practice?
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!
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