nanocompore
nanocompore copied to clipboard
tleonardi
RNA modifications detection from Nanopore dRNA-Seq data
Hi, Is it alright if I use one ctrl sample for all the replicates of an experiment? Having replicates makes sense if the IVT goes on the same flowcell as...
I note you have some capability in the API for specifying a list of transcript/ref accessions/ids to act as an exclude list. I cant see a CLI switch to provide...
Ideally scaling should be done for all kmers in a read to correct dwell-time shifts during the course of a run https://github.com/tleonardi/nanocompore/blob/62a8bf41712b5355519024786c5ba34b38ae36bb/nanocompore/TxComp.py#L195
Due to the way Nanocompore passes data between threads, when a transcript has a large amount of data associated with it (e.g. the transcript has very high coverage or is...
Data for the two conditions should be concatenated before scaling. As it is now, the two conditions are scaled separately, resulting in both conditions having mean 0. https://github.com/tleonardi/nanocompore/blob/9f8effec65cbd5347f5ac7e1625164389adad866/nanocompore/SampCompDB.py#L841-L848
When multiple transcripts cover the same genomic coordinates nanocompore reports multiples lines per genomic position
For non parametric tests, Nanocompore performs 1 test or Dwell time and 1 test for intensity per position. I would be nice to combine both using the Hou's method An...
At the moment instead of throwing an exception we just add "!!!!" to the kmer.. It's a left over from an old debugging session, but now it needs to be...
It looks like nanocompore sometimes spawns more threads than it should.. Starting it with nthreads=4 with the 7SK IVT data starts 16 threads.