This is a special usage mode of StringTie, distinct from the assembly usage mode. In the merge mode, StringTie takes as input a list of GTF/GFF files and merges/assembles these transcripts into a non-redundant set of transcripts. This mode is used in the new differential analysis pipeline to generate a global, unified set of transcripts (isoforms) across multiple RNA-Seq samples. If a reference annotation is provided, StringTie will assemble the transfrags from the input GTF files with the reference transcripts.
stringtie <aligned_reads.bam> [options]*
-G
-o
-m
-c
-F
-T
-f
-g
-i keep merged transcripts with retained introns; by defaultthese are not kept unless there is strong evidence for them
-l