mkdir Macrostomum_lignano_mixed_population_grown_under_standard_conditions-pooled-STAR-2.5.3a; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --limitSjdbInsertNsj 10000000 --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Plathelminthes/Macrostomum_lignano-Mlig_3_7/STAR --outFileNamePrefix Macrostomum_lignano_mixed_population_grown_under_standard_conditions-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Macrostomum_lignano_mixed_population_grown_under_standard_conditions-pooled.end1.fastq.gz Macrostomum_lignano_mixed_population_grown_under_standard_conditions-pooled.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Plathelminthes/Macrostomum_lignano-Mlig_3_7/GCA_002269645.1_Mlig_3_7_genomic.gtf --runThreadN 20 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 50 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigStrand Stranded  --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 500000000000