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**Operating system**
Linux OS
**Package name**
pbfusion-visualize_fusion.py
**Conda environment**
I set up the conda environment with python 3.8.19 and downloaded packages required for visual…
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I tested on the test dataset of nextneopi (https://github.com/icbi-lab/nextNEOpi). I has a similar session for using the arriba to get the fusion genes. From those fusion genes, it can get the peptide…
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I am investigating many fusions and have created a list of fusion candidates containing 1974 fusions. Of these, one of them is a true positive, also called by star fusions correctly. However, FusionIn…
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### Description of the bug
```bash
nextflow run main.nf \
-ansi-log false \
-profile docker,gcp \
-work-dir gs://path/to/bucket/scrnaseq/work \
--input samples.csv \
--protocol…
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Hi,
I had ~37.8 million Illumina paired end sequencing reads (Plant whole genome with chloroplast and mito genome included). I tried assembling the Chloroplast genome where around 4.39 million read…
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I have successfully installed the STAR v2.7.2a and STAR-Fusion v1.7.0, but I get the error:
```
Can't locate Set/IntervalTree.pm in @INC (you may need to install the Set::IntervalTree module) (@INC …
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Hi there,
I apologize for the naive question I'm about to ask, but I've been struggling with this for a week and would appreciate some help. I created a custom gene index using a FASTA file of fusi…
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Objectives of the tool:
- Create a subdirectory to store the essential information (files) needed for review
- Create a Tiered and Annotated report table that makes it more clear which fusion cand…
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-sample contains 131994
* Running CMD: /home/greenland/anaconda3/envs/fusion/lib/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /home/greenland/LZY/Fusion/CTAT_lib/GRCh38_…
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Hiya,
Can Arriba be used to detect fusions in single-cell RNAseq data (e.g. Smart-seq2). I expect to see a greater number of false positives compared to bulk RNAseq, and with a lower number of read…