From 86e4933b1aa85a5b77b0cfdd3f2aa81f1e9f22ad Mon Sep 17 00:00:00 2001 From: Heng Li Date: Fri, 2 Feb 2018 14:12:30 -0500 Subject: [PATCH] Added TOC --- misc/README.md | 23 ++++++++++++++--------- 1 file changed, 14 insertions(+), 9 deletions(-) diff --git a/misc/README.md b/misc/README.md index 49b14d2..2750409 100644 --- a/misc/README.md +++ b/misc/README.md @@ -13,6 +13,11 @@ minimap2 -cx splice ref.fa rna-seq.fq | splice2bed.js - # convert splice aln t - [Getting Started](#started) - [Introduction](#intro) - [Use Cases](#usage) + - [Convert PAF to other formats](#paf2aln) + - [Convert SAM to PAF](#sam2paf) + - [Convert GTF/GFF3 to BED12 format](#gff2bed) + - [Convert spliced alignment to BED12](#splice2bed) + - [Convert spliced alignment to BED12](#eval) ## Introduction @@ -25,31 +30,31 @@ curl -L https://github.com/attractivechaos/k8/releases/download/v0.2.4/k8-0.2.4. cp k8-0.2.4/k8-`uname -s` k8 ``` It is highly recommended to copy the executable `k8` to a directory on your -`PATH` such as `/usr/bin/env` can find them. +`PATH` such as `/usr/bin/env` can find it. ## Use Cases -### paf2aln.js: convert PAF to other formats +### Convert PAF to other formats Script [paf2aln.js](paf2aln.js) converts PAF with the [cs tag][cs] to [MAF][maf] or BLAST-like output. It only works with minimap2 output generated using the `--cs` tag. -### gff2bed.js: convert GTF/GFF3 to BED12 format +### Convert SAM to PAF + +Script [sam2paf.js](sam2paf.js) converts alignments in the SAM format to PAF. + +### Convert GTF/GFF3 to BED12 format Script [gff2bed.js](gff2bed.js) converts GFF format to 12-column BED format. It seamlessly works with both GTF and GFF3. -### splice2bed.js: convert spliced alignment to BED12 +### Convert spliced alignment to BED12 Script [splice2bed.js](splice2bed.js) converts spliced alignment in SAM or PAF to 12-column BED format. -### sam2paf.js: convert SAM to PAF - -Script [sam2paf.js](sam2paf.js) converts alignments in the SAM format to PAF. - -### 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