Liang Ou

SquiggleKit can be used for extract raw current signal in specific position of read?

3

Hi Thank you for you developing & maintaining this project :) I noticed that `squigglekit` can extract the current signal for a particular motif. So,I just wonder if it can...

Hi: I've trained a model.To evaluate the performance of the model, I used unused experimental samples and control samples as test sets. As a result, I find that the model...

OSerror when I tried to use trained model file to predict test data

5

Hi: I tried to predict the labels of test set by using the following command for evaluate the performance of custom mod-base model. ``` basecall.py --device 0 --modified_base_output basecalls.hdf5 "/root/test_data_7.17/fast5/"...

The prediction results showed a low recall

11

Hi: As I said in the previous issues,I'm trying to use taiyaki to train my modified RNA model.But I found the prediction results showed a low recall.I'll go through the...

How to quickly extract the relevant data of multiple regions of genome

3

Hi: Recently, I often need to use `tombo API `to extract data in many regions (such as the mean electrical signal value). It seems that this class `tombo.tombo_helper.intervalData` Only one...

IndexError:index is out of bounds

3

Hi Marcus When tombo re-squiggle a ` fast5_fn`, which has been `annotate_raw_with_fastqs` by tombo. An fast5 file in folder raised an unexpected error. ``` BaseCalled_template:::/home/weir/covid19_nanopore/raw_data/kim_rawdata/8F6N9/single_fast5/IVT/372/7b86be7e-3212-4cc9-804d-248094721897.fast5 ::: Traceback (most recent call...

curl error

3

Hi: I encountered this error when trying to download a large folder ``` Requesting folder 'Vero-Infected' from OSF Downloading Vero-Infected.zip Downloading: 30 GB Error in curl::curl_fetch_disk(x$url$url, x$disk, handle = x$url$handle)...

ConnectionError of osf clone

7

Hi: When I tried to clone an large size public project. The following error occurred with the opportunity: ``` requests.exceptions.ConnectionError: ('Connection aborted.', RemoteDisconnected('Remote end closed connection without response')) ``` How...

Hello velocyto maintainers, I am working with a dataset where the barcodes (CB) and UMIs (UR) are not in the standard string sequence format. Specifically, my barcodes are represented as...

bamtools split ERROR: could not open basecalls.sort.REF_NM_001019297.2.bam for writing.

1

Hi: When I run the following command：`bamtools split -in basecalls.sort.bam -reference` This error occurred: ``` bamtools split ERROR: could not open basecalls.sort.REF_NM_001019297.2.bam for writing. ``` So few error messages that...