Utilities

Standalone command-line utilities installed with nexus.

Command	Description
nexus_convert_netmhcpan_txt2tsv	Convert NetMHCpan TXT output file to a TSV file.
nexus_convert_scrna_bam2fastq	Convert an unaligned BAM file to a FASTQ.
nexus_count_scrna_assembly_support	Count cell and molecule support for each transcript from assembled from scRNA-seq.
nexus_create_abra2_targets_bed_file	Creates an ABRA2 targets BED file based on a GENCODE GTF file.
nexus_filter_rnabloom2_transcripts	Filter RNA-Bloom2 assembled transcripts.
nexus_filter_scrna_assembly	Filter scRNA-seq assembly based on minimum cell and molecule support.
nexus_filter_unspliced_transcripts	Filter unspliced transcripts.
nexus_find_scrna_barcode_knee	Find the knee of the barcode rank plot from an unaligned scRNA-seq BAM file.