neusomatic

neusomatic copied to clipboard

Hello, I'm new in the field of bioinformatics and my thesis will be about Neusomatic and the work it can do. The first step that needs to be accomplished is...

BlinkPSAhad

Formatting python scripts with black auto-formatter

1

Formatting changes with black auto-formatter.

pavan-kotha-strandls

Extended standalone

2

Use extra features in both standalone and ensemble modes.

msahraeian

Ensemble mode issue

1

Hi. I tried to run ensemble mode neusomatic. Since there was no 'SomaticSeq.Wrapper.sh' on 'https://github.com/bioinform/somaticseq/blob/master/SomaticSeq.Wrapper.sh', I ran 'somaticseq_parallel.py' using recommended command on 'https://github.com/bioinform/somaticseq/' and got 'Ensemble.sSNV.tsv' However, when I tried...

JunhakAhn

/bin/scan_alignments Not Found

1

Hi , I met "OSError: File not found: ../bin/scan_alignments" when I ran run_test.sh Is this file missed in the source code?

ghost

testing pretrined model

7

Hello, I tested my data and dream_challenge data with all the pre-trained model than you provided. The test results show that the recall rate is very low, less than 50%,...

bingdiao-zbw

Postprocess dedup filter

1

Multiple bug fixes and improvements

msahraeian

Remove pybedtools dependency

msahraeian

How to access CGC files?

1

Hi and thank you very much for the wonderful work you provided with NeuSomatic and SEQC-II. I would like to use SEQC-II for benchmarking, without having to realign or run...

GolfDeltaFox

Error: unable to open file or unable to determine types for file synthetic.vcf

31

Hi, I am trying to run neusomatic in ensemble mode, but got stuck after the SomaticSeq.Wrapper.sh step and at the "preprocess.py --mode train" step. I get the following error Error:...

gianfilippo