search

NKI-CCB / imfusion

Tool for identifying transposon insertions and their effects from RNA-seq data.
MIT License
5 stars 1 forks source link

SA or SD for building the reference #4

Open hshcao opened 5 years ago

hshcao commented 5 years ago

Hi there, I am building the augmented reference for identifying transposition activity in a bacterial genome using RNAseq data. I have the locations and sequences of the transposons in the host genome (name, start, end, strand, length), not sure what the SA and SD are available. [2019-07-07 22:44:04] Copying transposon files here are the err mesage I got: Traceback (most recent call last): File "/home/hcao/miniconda2/envs/imfusion/bin/imfusion-build", line 11, in load_entry_point('imfusion==0.3.2', 'console_scripts', 'imfusion-build')() File "/home/hcao/miniconda2/envs/imfusion/lib/python3.6/site-packages/imfusion/main/build.py", line 35, in main output_dir=args.output_dir) File "/home/hcao/miniconda2/envs/imfusion/lib/python3.6/site-packages/imfusion/build/indexers/base.py", line 161, in build build_util.check_feature_file(transposon_features_path) File "/home/hcao/miniconda2/envs/imfusion/lib/python3.6/site-packages/imfusion/build/util.py", line 239, in check_feature_file raise ValueError('No valid features (with type = SD or SA)' ValueError: No valid features (with type = SD or SA)were found in the transposon feature file.

is there anyway to build the reference without the SA or SD type information?

Thanks,

HC