nexus_create_abra2_targets_bed_file

Creates an ABRA2 targets BED file based on a GENCODE GTF file. The following tasks are performed: 1. Fetch all exon regions. 2. Drop duplicates and sort the exon regions. 3. Output the DataFrame to a BED file. 4. Merge regions by bedtools.

Usage

nexus_create_abra2_targets_bed_file \
    --gencode_gtf_file /path/to/file.gtf \
    --bedtools "" \
    --output_temp_bed_file /path/to/file.bed \
    --output_bed_file /path/to/file.bed

Parameters

Parameter	Type	Default	Description
--gencode_gtf_file	str	required	Input GENCODE GTF file including path (e.g. //gencode_.gtf).
--bedtools	str	required	bedtools path (e.g. //bedtools.static.binary).
--output_temp_bed_file	str	required	Output temp BED file including path (e.g. //gencode__abra2_targets_temp.bed).
--output_bed_file	str	required	Output BED file including path (e.g. //gencode__abra2_targets.bed). This is the final BED file that should be used as input for ABRA2.