Hi @kdsung
Your starting data appear to be the hifi_reads.bam described here reads.bam | CCS Docs.
HIFI reads are not paired end sequencing. These can be thought of as really long high quality “single end” reads … but in actuality these are reads that are each a mini-assembly.
So – punch line – exact the reads using the single end options. Maybe review how others are doing this, since the defaults might not produce exactly what you want.
Beyond that, you seem to have at least two different sample replicates in your history so far.
We have an example of this sort of workflow in our GTN Tutorials.
With all Assembly tutorials here
And a protocol developed by the UseGalaxy.org.au and other Australian scientists (the Galaxy workflows should work on any public UseGalaxy server)
With the top level VGP introduction here. I’m not sure of your species, but maybe interesting anyway.
Summary of what I would suggest
- Run through at least this tutorial. Really, it will help with making use of the other Galaxy resources so much easier. It takes maybe an hour? SO worth it.
Then:
- Copy your original two uploaded BAMs into a brand new history and then purge your original history (you don’t need any of that since you are starting over from a correct data extraction step).
- If you have more BAMs from other samples, also load those into your new history. You can process all together.
- Then put the BAMs into a collection folder (a list of similar datasets), then extract the reads.
- Remember to do read QA on any raw read data. Assembly is very sensitive to read quality! You won’t like the results if you skip this, assuming the job will even process with raw data (very good chance it won’t).
- Now, with prepared HIFI reads, you can think about any reference data you want to incorporate and any short reads you may want to incorporate.
- Then you can think about how to assemble: choosing the correct tool for your read types and reference data (if any).
Hope this helps!