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more doc in misc

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Heng Li 2018-02-02 14:07:17 -05:00
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misc/README.md
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@ -8,7 +8,13 @@ gff2bed.js anno.gtf | less -S # convert GTF/GFF3 to BED12
minimap2 -cx splice ref.fa rna-seq.fq | splice2bed.js - # convert splice aln to BED12 minimap2 -cx splice ref.fa rna-seq.fq | splice2bed.js - # convert splice aln to BED12
``` ```
## Introduction ## Table of Contents
- [Getting Started](#started)
- [Introduction](#intro)
- [Use Cases](#usage)
## <a name="intro"></a>Introduction
This directory contains auxiliary scripts for format conversion, mapping This directory contains auxiliary scripts for format conversion, mapping
accuracy evaluation and miscellaneous purposes. These scripts *require* accuracy evaluation and miscellaneous purposes. These scripts *require*
@ -21,7 +27,7 @@ cp k8-0.2.4/k8-`uname -s` k8
It is highly recommended to copy the executable `k8` to a directory on your 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 them.
## Use Cases ## <a name="usage"></a>Use Cases
### paf2aln.js: convert PAF to other formats ### paf2aln.js: convert PAF to other formats
@ -29,6 +35,20 @@ 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 [MAF][maf] or BLAST-like output. It only works with minimap2 output generated
using the `--cs` tag. using the `--cs` tag.
### gff2bed.js: 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
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] Script [sim-pbsim.js](sim-pbsim.js) converts the MAF output of [pbsim][pbsim]
@ -37,7 +57,7 @@ to FASTQ and encodes the true mapping position in the read name in a format like
[sim-mason2.js](sim-mason2.js) converts [mason2][mason2] simulated SAM to [sim-mason2.js](sim-mason2.js) converts [mason2][mason2] simulated SAM to
FASTQ. FASTQ.
Script [sim-eval.js](sim-eval.js) evaluates mapped SAM/PAF. Script [sim-eval.js](sim-eval.js) evaluates mapped SAM/PAF. Here is example output:
``` ```
Q 60 32478 0 0.000000000 32478 Q 60 32478 0 0.000000000 32478
Q 22 16 1 0.000030775 32494 Q 22 16 1 0.000030775 32494