1.7.9

1.7.9
(1). Remove --repeat, using --no-repeat-index in default, because we got different outputs even using the same input and parameter when using --repeat. For example: hisat-3n ~/Ref/hg38/hg38_ucsc_with_chrL -q -1 UWA7648_CX182024_Idg_1_P1-2-K15-A15-R1.trimmed.fq.gz -2 UWA7648_CX182024_Idg_1_P1-2-K15-A15-R2.trimmed.fq.gz --directional-mapping-reverse --base-change C,T --no-spliced-alignment --no-temp-splicesite -t --new-summary --summary-file hisat3n_dna_summary.txt --threads 20| samtools view -b -q 0 -o hisat3n_dna.unsort.bam