XPORE-DATAPREP(1)

🦋 XPORE-DATAPREP(1) — User Commands 🦋

okay bestie, welcome to the XPORE-DATAPREP(1) page, living in the User Commands section, and it's giving nanopore girlboss energy. let's get into it 💅

✨ NAME ✨

xpore-dataprep — Nanopore analysis of differential RNA modifications 🧬🌸

💖 DESCRIPTION 💖

so basically, here's the vibe — this is the usage line, and it's iconic:

usage: xpore-dataprep [-h] --eventalign EVENTALIGN --summary SUMMARY --out_dir OUT_DIR
                      [--ensembl ENSEMBL] [--species SPECIES]
                      [--customised_genome] [--reference_name REFERENCE_NAME]
                      [--annotation_name ANNOTATION_NAME]
                      [--gtf_path_or_url GTF_PATH_OR_URL]
                      [--transcript_fasta_paths_or_urls TRANSCRIPT_FASTA_PATHS_OR_URLS]
                      [--skip_eventalign_indexing] [--genome] [--n_processes N_PROCESSES]
                      [--chunk_size CHUNK_SIZE] [--readcount_min READCOUNT_MIN]
                      [--readcount_max READCOUNT_MAX] [--resume]

lowkey that's a lot of flags but we're gonna go through every single one, no skips, no shortcuts, periodt ✨

🎀 required arguments 🎀

these ones are non-negotiable bestie. you literally cannot run without them.

• --eventalign EVENTALIGN — the eventalign filepath, aka the output from nanopolish. (default: None) 🔥
• --summary SUMMARY — the eventalign summary filepath, also the output from nanopolish. (default: None) ✨
• --out_dir OUT_DIR — where the output directory lives. (default: None) 💖

🌸 optional arguments 🌸

optional but make it make sense, yk? here's the whole roster:

• -h, --help — shows this help message and dips. iconic behaviour honestly 🫶
• --ensembl ENSEMBL — the ensembl version for gene-transcript mapping. (default: 91) 🧬
• --species SPECIES — which species you're doing ensembl gene-transcript mapping for. (default: homo_sapiens) 🌍
• --customised_genome — use this if a customised genome is provided. (default: False) 💅
• --reference_name REFERENCE_NAME — the fasta reference name. (default: None) 📛
• --annotation_name ANNOTATION_NAME — the gtf annotation name. (default: None) 🏷️
• --gtf_path_or_url GTF_PATH_OR_URL — gtf file path or url. (default: None) 🔗
• --transcript_fasta_paths_or_urls TRANSCRIPT_FASTA_PATHS_OR_URLS — transcript fasta paths or urls. (default: None) 🧚
• --skip_eventalign_indexing — skips indexing the eventalign nanopolish output. (default: False) ⏭️
• --genome — to run on Genomic coordinates. Without this argument, the program will run on transcriptomic coordinates. (default: False) 🗺️
• --n_processes N_PROCESSES — how many processes to run. (default: 1) ⚡
• --chunk_size CHUNK_SIZE — number of lines from nanopolish eventalign.txt for processing. (default: 1000000) 📦
• --readcount_min READCOUNT_MIN — minimum read counts per gene. (default: 1) 📉
• --readcount_max READCOUNT_MAX — maximum read counts per gene. (default: 1000) 📈
• --resume — with this argument, the program will resume from the previous run. (default: False) 🔁

gentle reminder bestie: --genome is the switch between genomic and transcriptomic coordinates. no --genome, no genomic mode. that's the whole tea ☕

👑 AUTHOR 👑

This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program. 🫶

and that's the whole page, babe — xpore-dataprep version 1.0, dated May 2021, and you absolutely ate that read-through 💖✨🎀 stay slaying, and go prep those data 🦋🌈⭐