Minor Suggestion for README.md of BERTE Demo: File Extension Consistency #1
Description
Dear Dr. Chen,
I hope this message finds you well. My name is Iamil Ferrer Pomer, and I am a Master's student in Bioinformatics and Biostatistics at the Universitat Oberta de Catalunya (UOC). I am currently working on my Master's Thesis, which focuses on Deep Learning applications for transposon analysis. I have been exploring your BERTE tool as part of my research, and I would like to express my gratitude for making this valuable resource available to the community.
While following the demo pipeline, I noticed a minor inconsistency in the README.md file that caused an error during execution. Specifically, in Step 3, the output files are generated with the .jsonl extension (e.g., demo_SINE_506bp_bothend_kmer_fragments_cls.jsonl). However, in Step 4, the jsonl_to_txt.py script is called without the .jsonl extension (e.g., demo_SINE_506bp_bothend_kmer_fragments_cls). This mismatch caused an error when I tried to run the pipeline as described.
To resolve this, I would like to humbly suggest modifying Step 3 to remove the .jsonl extension from the --output_file parameter. This small adjustment would ensure that the pipeline runs smoothly without requiring changes to Step 4. Please let me know if this suggestion is appropriate or if I have misunderstood any part of the process.
Thank you again for your work on BERTE and for your attention to this matter. I deeply admire your contributions to the field, and I am grateful for the opportunity to learn from and build upon your tool in my research.
Best regards,
Iamil Ferrer Pomer
Master's Student in Bioinformatics and Biostatistics
Universitat Oberta de Catalunya (UOC)