Jared Simpson
Jared Simpson
Sorry @lkerr34 but I don't have a script to convert in that direction. If you have experience in python though, you might want to take a look at pysam's support...
Sorry for not answering this before. It looks like you passed in the `.bai` file as the bam argument?
This is likely due to nanopolish not supporting RNA004. Now that dorado calls poly-A tail lengths, we are no longer updating this tool.
Can you provide the exact nanopolish commands that you ran?
That looks OK - what messages were printed to the terminal for each command?
Hi @wuy24, Nanopolish itself doesn't call m6A so I would consult with the package you are using for m6A identification. But in general yes, Us should be converted to Ts...
The HDF5 developers removed old source files from their FTP site which broke nanopolish's Makefile. I have just fixed this, can you try again with the latest code on github?
@zigavicic could you send the complete build log to me?
@valerieT1998 can you send me the complete output when you try to run `make`?
Those warnings are fine and expected, can you let it continue until it naturally stops?