lmulroney

Hi @sidizhao, It looks like you ran nanocompore on a genomic reference instead of a transcriptomic reference. Sometimes Nanocompore can stall when the reference sequences are super long (greater than...

Hi @sidizhao, Yes, by transcriptomic reference I mean a reference fasta file of each contiguous transcript isoform with no introns present, and one reference sequence per isoform. This is the...

You essentially need to start over from the minimap2 step using the transcriptome reference fasta instead of the genome reference fasta. This will require that you redo eventalign and eventalign...

You can try using f5c instead of nanopolish. It is a c implementation of nanopolish and is roughly 10 times faster. There are a few flags you need to use...

Hi @keenhl, That will largely depend on the experimental set up and which two samples your are comparing. In the case of a WT and a writer enzyme KO/KD, or...

Dear rezarahman12, Ttry again but after removeing: , log_level="warning" from your db instantiating line. Logan

Hi @kwonej0617, Just a quick question, In the eventalign_collapse.tsv snippet you shared, are the two data lines from the same file or the first data line from the two separate...

Hi @kwonej0617, Do you get the same "SystemError: null argument to internal routine" error if you try to run Nanocompore sampcomp outside of your script? I did a little digging...

@kwonej0617, I recommend checking your python installation in addition to your nanocompore installation. Logan

Hi @kwonej0617, It looks like all of the I/O errors happened during a write command, and not a read command. First thing I would do is make sure you didn't...