Comments (5)
zhengtaoxiao
commented on July 30, 2024
Hi,
Currently, the RiboCode only support the ensemble gtf file, for example,
ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz
It looks like the line of "gene" feature is missing in your gtf file.
from ribocode.
commented on July 30, 2024
Hi,
The GTF file was the one you recommend in your tutorial, the Ensemble one.
from ribocode.
zhengtaoxiao
commented on July 30, 2024
Hi,
Can you post the complete error message here ？
from ribocode.
commented on July 30, 2024
Hi,
I just removed the package and reinstalled with pip this time and it then worked flawlessly, not sure why though, exactly the same files were used.
Thanks!
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zhengtaoxiao
commented on July 30, 2024
RiboCode use pickle to store and load data. The version of variables and classes are pickled. If you update the RiboCode package, the pickle file should be regenerated.
from ribocode.
Related Issues (20)
- prepare_transcripts not taking multiple CDSs into account HOT 1
- ValueError: Can't transform the genomic interval, please check! HOT 1
- Read counts issues HOT 2
- ImportError: cannot import name 'PPoly' from partially initialized module 'scipy.interpolate' (most likely due to a circular import) (/home/zhai2/miniconda3/lib/python3.8/site-packages/scipy/interpolate/__init__.py) HOT 1
- plot_orf_density error,it show the following arguments are required: --start-codon
- No obviously periodicity are detected from bam file, it could be due to poor quality sequencing. Please check the metagene plots and try again by lowering the value of frame0_percent HOT 1
- can't locate attribute: psites_number HOT 1
- RiboCode_onestep crashes when calling detectORF HOT 1
- Whether multiple mapping affect ribocode result HOT 1
- error in metaplots step HOT 1
- 请问关于ORF预测结果中‘Psites_frame0_RPKM’代表什么意思？ HOT 4
- Empty "transcripts_cds.txt" file HOT 1
- remove PCR duplicate HOT 2
- TypeError: '<' not supported between instances of 'str' and 'NoneType' HOT 2
- Question on adjusted P values reported in collapsed output HOT 2
- different transcripts of one gene
- ModuleNotFoundError: No module named 'fasta' HOT 6
- ValueError: unsupported pickle protocol: 5 in metaplots HOT 1
- psites_number table is not generated with v1.2.15
- Error, the references in bam are different from transcriptome annotation
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