RSEM-PL...WIGGLES(1)

💖 rsem-plot-transcript-wiggles 💖

okay bestie, so this one is a script that comes bundled with the User Contributed Perl Documentation — it's literally called rsem-plot-transcript-wiggles, and it makes cute little wiggle plots for your transcripts and genes. it's giving very much "let me draw your read depth for you" energy. ✨

---

🌸 NAME 🌸

rsem-plot-transcript-wiggles — bestie, this generates PDF wiggle plots from either transcript ids or gene ids. that's the whole job. she does it well too. 💅

---

🎀 SYNOPSIS 🎀

rsem-plot-transcript-wiggles [options] sample_name input_list output_plot_file

three positional arguments and a lil pile of optional flags, and you're off. no cap.

---

🦋 ARGUMENTS 🦋

here's the tea on the three things you must hand over, in this order:

• sample_name — the name of the sample you analyzed. that's it, that's the vibe. this is the string everything downstream gets named after. 👑
• input_list — a list of transcript ids or gene ids. important: it cannot be a mixture of transcript ids and gene ids, so pick a lane, bestie. 😭 each id goes on its own line, with no extra spaces. respect the format pls.
• output_plot_file — the file name of the pdf file that holds all your plots. everything goes in here. one file, all the plots, like a lil scrapbook. 🎀

---

✨ OPTIONS ✨

every flag, every default, nothing skipped. this is the part where i tell you everything and you pretend you're gonna remember it:

• --gene-list — tells her that your input_list is a list of gene ids. (Default: off)
• --transcript-list — tells her that your input_list is a list of transcript ids. heads up: you can only turn this one on if allele-specific expression is calculated. otherwise she's not gonna be into it. (Default: off)
• --show-unique — makes the wiggle plots show up as stacked bar plots instead. scroll down to the DESCRIPTION section for the full breakdown, because the colors matter here. (Default: off)
• -p/--num-threads <int> — set the number of threads we can use. more threads = more hands on deck. (Default: 1)
• --memory-per-thread <string> — set the maximum allowable memory per thread. <string> is the memory amount, and it accepts the suffixes 'K/M/G' — so like 1G, 500M, etc. she'll take what you give her. (Default: 1G)
• -h/--help — show help information. the classic. when in doubt, ask for help, bestie. 🫶

---

💜 DESCRIPTION 💜

okay so here's what's actually happening under the hood. this program generates transcript wiggle plots and drops them all into a single pdf file. she can accept either a list of transcript ids or a list of gene ids (the gene id route needs transcript-to-gene mapping information to be provided), and she's got two modes for showing the plots.

mode one: if --show-unique is not specified, then the wiggle plot for each transcript is a plain histogram, where each position's height is the expected read depth at that position. simple. clean. iconic.

mode two: if --show-unique is specified, then for each transcript you get a stacked bar plot. and the color coding is important, so listen up:

• the read depth of unique reads (reads that have only one alignment) is shown in black.
• the read depth of multi-reads (reads that align to more than one place) is shown in red, stacked on top of the unique read depth.

⚠️ real talk warning: this program uses files that RSEM generated previously. so please, do not delete or move any file that rsem-calculate-expression generated. i am begging you. she needs them. she will not work without them. 😭

and one more thing: if allele-specific expression is calculated, the basic unit for plotting becomes an allele-specific transcript, and the plots can be grouped by either transcript ids (--transcript-list) or gene ids (--gene-list). choose your grouping, she handles the rest. 🦋

---

🌈 OUTPUT 🌈

output_plot_file

this is the pdf file containing all the plots she generated. here's the layout tea:

• if you gave her a list of transcript ids, each page displays at most 6 plots, arranged in 3 rows and 2 columns.
• if you gave her gene ids, each page displays one gene. that gene's id is shown at the top, and all its transcripts' wiggle plots get shown on that same page. the arrangement of plots is determined automatically — she's got taste, trust her.
• for each transcript wiggle plot, the transcript id is displayed as the title. the x-axis is position in the transcript, and the y-axis is read depth. periodt.

and if allele-specific expression is calculated, the basic unit becomes an allele-specific transcript, and transcript ids and gene ids can be used to group those allele-specific transcripts. same energy, new unit. 💅

sample_name.transcript.sorted.bam and sample_name.transcript.readdepth

if these two files don't exist, rsem-plot-transcript-wiggles will automatically generate them for you. she's self-sufficient like that. ✨

sample_name.uniq.transcript.bam, sample_name.uniq.transcript.sorted.bam and sample_name.uniq.transcript.readdepth

if the --show-unique option is specified and these files don't exist, rsem-plot-transcript-wiggles will automatically generate them too. three files, all hers, all handled. 🎀

---

🌸 EXAMPLES 🌸

okay let's say sample_name is set to 'mmliver_single_quals' and output_plot_file is set to 'output.pdf'. and input_list is set to 'transcript_ids.txt' if you're giving transcript ids, or 'gene_ids.txt' if you're giving gene ids. got it? slay, let's go. 🫶

1) you're giving transcript ids and you just want normal wiggle plots:

rsem-plot-transcript-wiggles mmliver_single_quals transcript_ids.txt output.pdf

basic, clean, does the thing. 💖

2) you're giving gene ids and you want the stacked bar plot situation:

rsem-plot-transcript-wiggles --gene-list --show-unique mmliver_single_quals gene_ids.txt output.pdf

two flags, one command, stacked bars in red and black, absolutely ate. 🔥

---

👑 SEE YOU LATER 👑

that's the whole page, bestie. this one's from the User Contributed Perl Documentation collection and it's perl v5.38.2, dated 2024-04-14 — so like, vintage in a cool way, not in a dusty way. go make some wiggle plots. i'm obsessed with you. mwah 💋