Use when aligning RNA-seq or genomic DNA-seq reads to a reference index. Supports paired-end and single-end reads in FASTQ, FASTA, SAM, or BAM formats.
subread-align -i <index_name> -r <input> -t <type> -o <output>/home/vimalinx/miniforge3/envs/bio/bin/subread-alignsubjunc instead when exon-exon junction detection is central.# 1) Genomic DNA-seq alignment
subread-align \
-i ref_index \
-r reads.fastq.gz \
-t 1 \
-o sample.bam \
-T 8
# 2) Paired-end RNA-seq alignment
subread-align \
-i ref_index \
-r sample_R1.fastq.gz \
-R sample_R2.fastq.gz \
-t 0 \
-o sample.bam \
-T 8
# 3) Coordinate-sorted BAM ready for genome-browser loading
subread-align \
-i ref_index \
-r sample_R1.fastq.gz \
-R sample_R2.fastq.gz \
-t 1 \
-o sample.bam \
-T 8 \
--sortReadsByCoordinates
subread-buildindex and keep the basename stable.-t 0 for RNA-seq and -t 1 for genomic DNA before tuning anything else.-i, -r, and -t are mandatory, and -i expects the index basename, not the FASTA file.--SAMinput or --BAMinput only for alignment-file input.--SAMoutput only if plain-text SAM is actually needed.--multiMapping changes reporting behavior substantially; pair it with -B intentionally.-m, -p, -M, and -I affect sensitivity and specificity, so keep those settings cohort-consistent.