Combining short and long reads with StringTie --mix

[Jason-Eigenbrood]

Ask away!

How would you recommend implementing the StringTie --mix parameter in the pipeline? (To use both short and long reads). I have the pipeline working on the cluster normally. I am wondering where could I put the short-read bam alignments so they are pulled in (in same directory as normal?), and how could I update the stringtie command to "stringtie --mix -o mix_reads.out.gtf short.bam long.bam" ensuring the short reads are called first?

[nrhorner]

Hi Jason,

It would take some reworking of the workflow to be able to do this, but there are no plans at the moment to include this feature.