REAPR-PERFECTFROMBAM(1)

📦
version 1.0.18 · 5 versions
, in ubuntu resolute, ubuntu stonking

💖 REAPR-PERFECTFROMBAM 💖

okay bestie, welcome to the reapr-perfectfrombam(1) page — it's the manual page for the bit of REAPR that goes "hey, what if we made a perfect mapping depth file from a BAM?" and you're gonna understand all of it, i promise 🫶

✨ NAME ✨

reapr-perfectfrombam — generate perfect mapping plots from a bam file 🌸

✨ SYNOPSIS ✨

reapr perfectfrombam [options] <in.bam> <outfileprefix> <mininsert>
<maxinsert> <repetitive-max-qual> <perfect-min-qual>
<perfect-min-alignment-score>

✨ DESCRIPTION ✨

so basically this is the alternative to using perfectmap, for large genomes. that's the whole vibe of it.

It takes a BAM, and like — that BAM must have AS:... tags in each line. non-negotiable, it needs those. Then it makes a file of perfect mapping depth, which you use with the REAPR pipeline. 💅

genuinely though, the recommendation is to use perfectmap instead, unless your genome is large (more than ~300MB). why? because even though reapr perfectmap is very fast to run, it uses a lot of memory. so it's giving speed, but at the cost of RAM. pick your fighter. 💀

A BAM file made by smaltmap is suitable input. ✅

Reads in pair pointing towards each other, with the given minimum alignment score and mapping quality and within the given insert size range are used to generate the coverage across the genome. like, those are the reads that get to count. everyone else is a background character. ✨

Additionally, regions with repetitive coverage are called, by taking read pairs where at least one read of the pair (is mapped and) has mapping quality less than or equal to <repetitive max qual>. 🌀

✨ OPTIONS ✨

  • -noclean — Use this to not delete the temporary bam file. (yes bestie, that temporary bam file wants to be cleaned up by default — this flag is you saying "no, keep it, i need it" 🙈)

✨ SEE ALSO ✨

and that's the whole thing, no cap — you're now certified in reapr-perfectfrombam 💅✨

sign-off time: this was the REAPR-PERFECTFROMBAM(1) manual page (source: REAPR), so go forth and map perfectly, you absolute icon 👑🦋

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