About the annotation used in 4th script. GTF or BED?

[gxAlan233]

Hello, I have a question about the 4th script.
In the Reference requirements, the required annotation file listed is:
Comprehensive gene annotation: gencode.v40.annotation.gtf (and/or the most recent version)

But in the description of 4th script ( L1 Detection Part 2: Mapping Reads with LINE/L1 Elements Detected to the hg38 Reference Genome)
The required annotation file is BED rather than GTF:
REF_SPLICE=../references/gencode.v40.annotation.bed

Is it meaning that I need to convert GTF to BED before run the 4th script?

[gxAlan233]

Besides, I found another problem that the LongReadSum v1.3.0 requires python >= 3.9, while the python listed in the pipeline is 3.7.11. So maybe 2 conda environments for different python are necessary?

[karleenarybacki]

Hello! Apologies for the delayed response. Yes, the required references should include the BED format of the GTF file to be used in the fourth script. Different Python versions may be required for various parts of the pipeline, so setting up separate conda environments is advisable. Thank you for catching these points!