99 lines
4.1 KiB
Markdown
99 lines
4.1 KiB
Markdown
## <a name="started"></a>Getting Started
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```sh
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curl -L https://github.com/attractivechaos/k8/releases/download/v0.2.4/k8-0.2.4.tar.bz2 | tar -jxf -
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cp k8-0.2.4/k8-`uname -s` k8 # or better copy to a directory on PATH
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minimap2 --cs test/MT-*.fa | paf2aln.js - | less # pretty print base alignment
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sam2paf.js aln.sam.gz | less -S # convert SAM to PAF
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gff2bed.js anno.gtf | less -S # convert GTF/GFF3 to BED12
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minimap2 -cx splice ref.fa rna-seq.fq | splice2bed.js - # convert splice aln to BED12
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```
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## Table of Contents
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- [Getting Started](#started)
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- [Introduction](#intro)
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- [Use Cases](#usage)
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- [Convert PAF to other formats](#paf2aln)
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- [Convert SAM to PAF](#sam2paf)
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- [Convert GTF/GFF3 to BED12 format](#gff2bed)
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- [Convert spliced alignment to BED12](#splice2bed)
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- [Evaluating mapping accuracy with simulated reads](#mapeval)
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- [Evaluating read overlap sensitivity](#oveval)
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## <a name="intro"></a>Introduction
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This directory contains auxiliary scripts for format conversion, mapping
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accuracy evaluation and miscellaneous purposes. These scripts *require*
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the [k8 Javascript shell][k8] to run. On Linux or Mac, you can download
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the precompiled k8 binary with:
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```sh
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curl -L https://github.com/attractivechaos/k8/releases/download/v0.2.4/k8-0.2.4.tar.bz2 | tar -jxf -
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cp k8-0.2.4/k8-`uname -s` k8
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```
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It is highly recommended to copy the executable `k8` to a directory on your
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`PATH` such as `/usr/bin/env` can find it.
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## <a name="usage"></a>Use Cases
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### <a name="paf2aln"></a>Convert PAF to other formats
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Script [paf2aln.js](paf2aln.js) converts PAF with the [cs tag][cs] to
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[MAF][maf] or BLAST-like output. It only works with minimap2 output generated
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using the `--cs` tag.
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### <a name="sam2paf"></a>Convert SAM to PAF
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Script [sam2paf.js](sam2paf.js) converts alignments in the SAM format to PAF.
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### <a name="gff2bed"></a>Convert GTF/GFF3 to BED12 format
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Script [gff2bed.js](gff2bed.js) converts GFF format to 12-column BED format. It
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seamlessly works with both GTF and GFF3.
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### <a name="splice2bed"></a>Convert spliced alignment to BED12
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Script [splice2bed.js](splice2bed.js) converts spliced alignment in SAM or PAF
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to 12-column BED format.
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### <a name="mapeval"></a>Evaluating mapping accuracy with simulated reads
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Script [sim-pbsim.js](sim-pbsim.js) converts the MAF output of [pbsim][pbsim]
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to FASTQ and encodes the true mapping position in the read name in a format like
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`S1_33!chr1!225258409!225267761!-`. Similarly, script
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[sim-mason2.js](sim-mason2.js) converts [mason2][mason2] simulated SAM to
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FASTQ.
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Script [sim-eval.js](sim-eval.js) evaluates mapped SAM/PAF. Here is example output:
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```
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Q 60 32478 0 0.000000000 32478
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Q 22 16 1 0.000030775 32494
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Q 21 43 1 0.000061468 32537
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Q 19 73 1 0.000091996 32610
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Q 14 66 1 0.000122414 32676
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Q 10 27 3 0.000214048 32703
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Q 8 14 1 0.000244521 32717
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Q 7 13 2 0.000305530 32730
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Q 6 46 1 0.000335611 32776
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Q 3 10 1 0.000366010 32786
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Q 2 20 2 0.000426751 32806
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Q 1 248 94 0.003267381 33054
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Q 0 31 17 0.003778147 33085
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U 3
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```
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where each Q-line gives the quality threshold, the number of reads mapped with
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mapping quality equal to or greater than the threshold, number of wrong
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mappings, accumulative mapping error rate and the accumulative number of
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mapped reads. The U-line gives the number of unmapped reads if they are present
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in the SAM file.
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### <a name="oveval"></a>Evaluating read overlap sensitivity
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Script [ov-eval.js](ov-eval.js) takes read-to-reference alignment in PAF and
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read overlaps in PAF and evaluates the sensitivity.
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[cs]: https://github.com/lh3/minimap2#cs
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[k8]: https://github.com/attractivechaos/k8
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[maf]: https://genome.ucsc.edu/FAQ/FAQformat#format5
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[pbsim]: https://github.com/pfaucon/PBSIM-PacBio-Simulator
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[mason2]: https://github.com/seqan/seqan/tree/master/apps/mason2
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