what is the meaning of --dta paremeter used in the Hisat2 alignment?

Question

[mathavanbioinfo]

Hello All

Can any one explain the meaning of the parameter --dta eports alignments tailored for transcript assemblers in Hisat2 alignment tool

Answer 1

[Ram]

Did you read the manual? It states what and why clearly:

-dta/--downstream-transcriptome-assembly

Report alignments tailored for transcript assemblers including StringTie. With this option, HISAT2 requires longer anchor lengths for de novo discovery of splice sites. This leads to fewer alignments with short-anchors, which helps transcript assemblers improve significantly in computation and memory usage.