akk01

Sample Fast5 where Tombo was tested

1

I have been trying to process my ONT data with Tombo, where I followed commands from tutorial. The pipeline fails at several steps, where some of them are solved after...

Trust4 output file format for VDJ visualization

9

With programs like Seurat and Scanpy + scirpy, we visualize the gene expression and VDJ data. I am wondering what output files from Trust4 can be used for the same...

Error with model download

5

📜 Retrieving model list from server https://celltypist.cog.sanger.ac.uk/models/models.json --------------------------------------------------------------------------- timeout Traceback (most recent call last) ~/.conda/envs/single_cell_v0.1/lib/python3.7/site-packages/urllib3/connectionpool.py in _make_request(self, conn, method, url, timeout, chunked, **httplib_request_kw) 381 try: --> 382 self._validate_conn(conn) 383 except...

ERROR:ont_fast5_api.conversion_tools.multi_to_single_fast5:Could not convert Multi->Single for file type 'single-read' with path

4

I am getting this error when I run `multi_to_single_fast5` with Fast5: `ERROR:ont_fast5_api.conversion_tools.multi_to_single_fast5:Could not convert Multi->Single for file type 'single-read' with path` How to check if the files are multi-fast5? What...