sample seqmode fq1 index_size kmer fq1_3p fq1_5p organism gtf genome sd mean multimappers soft_clip pass_mode libtype fq1_polya_3p fq1_polya_5p fq2 fq2_3p fq2_5p fq2_polya_3p fq2_polya_5p synthetic_10_reads_paired_synthetic_10_reads_paired pe ../input_files/project1/synthetic.mate_1.fastq.gz 75 31 AGATCGGAAGAGCACA XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/genome.fa 100 250 10 EndToEnd None ISF AAAAAAAAAAAAAAAAA XXXXXXXXXXXXXXXXX ../input_files/project1/synthetic.mate_2.fastq.gz AGATCGGAAGAGCGT XXXXXXXXXXXXX XXXXXXXXXXXXXXXXX TTTTTTTTTTTTTTTTT synthetic_10_reads_mate_1_synthetic_10_reads_mate_1 se ../input_files/project2/synthetic.mate_1.fastq.gz 75 31 AGATCGGAAGAGCACA XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/genome.fa 100 250 10 EndToEnd None SF AAAAAAAAAAAAAAAAA XXXXXXXXXXXXXXXXX XXXXXXXXXXXXX XXXXXXXXXXXXX XXXXXXXXXXXXX XXXXXXXXXXXXX XXXXXXXXXXXXX