Hi,
I want to apply -u f to force minimap2 to consider the forward transcript strand only for Nanopore Direct RNA seq analaysis. Does anyone know how to do this in Galaxy?
Thanks,
Natalia
Welcome, @natipinello
The -u option is on the tool form nested under Alignment options with the -slice option toggled to “yes”.
Screenshot
This is the description about how to use it in the Help.
Map long mRNA/cDNA reads
There are different long-read RNA-seq technologies, including tranditional full-length cDNA, EST, PacBio Iso-seq, Nanopore 2D cDNA-seq and Direct RNA-seq. They produce data of varying quality and properties. By default, -x splice assumes the read orientation relative to the transcript strand is unknown. It tries two rounds of alignment to infer the orientation and write the strand to the ts SAM/PAF tag if possible. For Iso-seq, Direct RNA-seq and tranditional full-length cDNAs, it would be desired to apply -u f to force minimap2 to consider the forward transcript strand only. This speeds up alignment with slight improvement to accuracy. For noisy Nanopore Direct RNA-seq reads, it is recommended to use a smaller k-mer size for increased sensitivity to the first or the last exons.
It is worth noting that by default -x splice prefers GT[A/G]…[C/T]AG over GT[C/T]…[A/G]AG, and then over other splicing signals. Considering one additional base improves the junction accuracy for noisy reads, but reduces the accuracy when aligning against the widely used SIRV control data. This is because SIRV does not honor the evolutionarily conservative splicing signal. If you are studying SIRV, you may apply --splice-flank=no to let minimap2 only model GT…AG, ignoring the additional base.
This is a bit tricky to find!
Options are nested to group functions that are logically related or dependent on each other. If you are not sure how that was done: try browser-searching the form. Expanding all the nested sections can help when doing this, and sometimes toggling an option is needed (it was for this one). 
We can help here if you or anyone gets stuck again with another complicated tool like this one.
Thank you Jenna! 
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