diff --git a/misc/README.md b/misc/README.md index 2750409..067738a 100644 --- a/misc/README.md +++ b/misc/README.md @@ -17,7 +17,8 @@ minimap2 -cx splice ref.fa rna-seq.fq | splice2bed.js - # convert splice aln t - [Convert SAM to PAF](#sam2paf) - [Convert GTF/GFF3 to BED12 format](#gff2bed) - [Convert spliced alignment to BED12](#splice2bed) - - [Convert spliced alignment to BED12](#eval) + - [Evaluating mapping accuracy with simulated reads](#mapeval) + - [Evaluating read overlap sensitivity](#oveval) ## Introduction @@ -54,7 +55,7 @@ seamlessly works with both GTF and GFF3. Script [splice2bed.js](splice2bed.js) converts spliced alignment in SAM or PAF to 12-column BED format. -### Evaluating mapping accuracy with simulated reads +### Evaluating mapping accuracy with simulated reads Script [sim-pbsim.js](sim-pbsim.js) converts the MAF output of [pbsim][pbsim] to FASTQ and encodes the true mapping position in the read name in a format like @@ -85,6 +86,11 @@ mappings, accumulative mapping error rate and the accumulative number of mapped reads. The U-line gives the number of unmapped reads if they are present in the SAM file. +### Evaluating read overlap sensitivity + +Script [ov-eval.js](ov-eval.js) takes read-to-reference alignment in PAF and +read overlaps in PAF and evaluates the sensitivity. + [cs]: https://github.com/lh3/minimap2#cs [k8]: https://github.com/attractivechaos/k8 [maf]: https://genome.ucsc.edu/FAQ/FAQformat#format5 diff --git a/misc/ov-eval.js b/misc/ov-eval.js old mode 100644 new mode 100755 index db8f2eb..7be4a5e --- a/misc/ov-eval.js +++ b/misc/ov-eval.js @@ -1,3 +1,5 @@ +#!/usr/bin/env k8 + var getopt = function(args, ostr) { var oli; // option letter list index if (typeof(getopt.place) == 'undefined')