Question about parameters for cleaned data

[GordonZ9494]

Hello All,

I was wondering what are some parameter (or all) to keep as much data as possible as I am working with cleaned data (removed low quality read and adapter). Below I had attempted to keep all of my data points but I am missing 20 k reads.
star --runThreadN 8 \ --genomeDir STAR_index \ --readFilesIn CleanData/LCS10477_Zh1_Clean_Data1.fq CleanData/LCS10477_Zh1_Clean_Data2.fq \ --outFileNamePrefix alignments_zh/N_C1_ \ --outSAMtype BAM SortedByCoordinate \ --sjdbOverhang max(ReadLength) -1 \ --alignIntronMin 1 \ --outFilterMultimapNmax 0 \ --outFilterMismatchNmax 0 \ --scoreDelOpen -2 \ --scoreInsOpen -2 \ --scoreDelBase -1 \ --scoreInsBase -1 \ --outSAMunmapped Within \ --outFilterType BySJout \ --outReadsUnmapped Fastx \ --outSAMprimaryFlag AllBestScore \ --outFilterScoreMinOverLread 0.0 \ --outFilterMatchNminOverLread 0.0 \ --outFilterMatchNmin 0 \ --outSAMattrRGline ID:group1 \ --limitOutSAMoneReadBytes 1000000 \ --outSAMattrIHstart 0 \ --alignEndsType Local \ --outFilterIntronMotifs None \ --alignSJoverhangMin 1 \ --alignSJDBoverhangMin 1 \ --chimSegmentMin 15 \ --chimJunctionOverhangMin 15 \ --quantMode TranscriptomeSAM GeneCounts \ --outSAMstrandField intronMotif \ --readFilesCommand zcat \ --outSAMmapqUnique 60 \ --winAnchorMultimapNmax 200 \ --readFilesInMemory