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Heng Li 2018-02-02 14:12:30 -05:00
parent a633a744b6
commit 86e4933b1a
1 changed files with 14 additions and 9 deletions
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misc/README.md
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@ -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)
## <a name="intro"></a>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.
## <a name="usage"></a>Use Cases
### paf2aln.js: convert PAF to other formats
### <a name="paf2aln"></a>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
### <a name="sam2paf"></a>Convert SAM to PAF
Script [sam2paf.js](sam2paf.js) converts alignments in the SAM format to PAF.
### <a name="gff2bed"></a>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
### <a name="splice2bed"></a>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
### <a name="eval"></a>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