Yuk Kei Wan

Hi Yanan(@ynren1020), If I understand your question correctly, you want to convert the transcript position to the genome coordinate. You can use the `--genome` flag with `gtf` and `fasta` provided...

Hi Yanan(@ynren1020), No problem! Glad to help! Do you mind sharing the top 10 lines of your `eventalign.txt` file by `head eventalign.txt`, please? You can also check whether you used...

Hi Yanan(@ynren1020), Do you mind pasting the several lines of your eventalign.txt file directly in the message, please? I don't see the attachment of the first few lines of your...

Hi Yanan(@ynren1020), The first column of your `eventalign.txt` file should be only the transcript_id (e.g. ENST00000457540.1), so you will have to remove the information after the transcript_id. Here is an...

Hi @ynren1020, Sorry for the delayed reply! (I just saw your comment) You can find the preprocessing steps prior to running `xpore dataprep` here: https://xpore.readthedocs.io/en/latest/preparation.html Thanks! Best wishes, Yuk Kei

Hi @acurry-hyde, `xpore dataprep` does not support the contig being in the following format: ``` ENST00000457540.1|ENSG00000225630.1|OTTHUMG00000002336.1|OTTHUMT00000006718.1|MTND2P28-201|MTND2P28|1044|unprocessed_pseudogene| ``` You will have to change the eventalign contig column to include only the...

Hi @dywang0323, Do you mind showing the first 10 lines of your `hbecpolya_event.tsv` file, please? `head hbecpolya_event.tsv` Thanks! Best wishes, Yuk Kei

Hi @DrDaedalusWHU, Thank you so much for leaving an issue. The `demo.gtf` and `demo.fa` from zenodo's `demo.tar.gz` are in `html` format, which @ploy-np will update those files on zenodo soon....

Hi @Wardale24, ``` /home/alex/.local/lib/python3.8/site-packages/xpore/scripts/dataprep.py:72: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats...

Not a problem at all, @Wardale24 !