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explained --junc-bed in README

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Heng Li 2021-03-06 19:44:24 -05:00
parent ecbc399fa2
commit 1c4b7e8a48
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14
README.md
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@ -19,6 +19,7 @@ cd minimap2 && make
./minimap2 -ax splice ref.fa rna-reads.fa > aln.sam # spliced long reads (strand unknown) ./minimap2 -ax splice ref.fa rna-reads.fa > aln.sam # spliced long reads (strand unknown)
./minimap2 -ax splice -uf -k14 ref.fa reads.fa > aln.sam # noisy Nanopore Direct RNA-seq ./minimap2 -ax splice -uf -k14 ref.fa reads.fa > aln.sam # noisy Nanopore Direct RNA-seq
./minimap2 -ax splice:hq -uf ref.fa query.fa > aln.sam # Final PacBio Iso-seq or traditional cDNA ./minimap2 -ax splice:hq -uf ref.fa query.fa > aln.sam # Final PacBio Iso-seq or traditional cDNA
./minimap2 -ax splice --junc-bed anno.bed12 ref.fa query.fa > aln.sam # prioritize on annotated junctions
./minimap2 -cx asm5 asm1.fa asm2.fa > aln.paf # intra-species asm-to-asm alignment ./minimap2 -cx asm5 asm1.fa asm2.fa > aln.paf # intra-species asm-to-asm alignment
./minimap2 -x ava-pb reads.fa reads.fa > overlaps.paf # PacBio read overlap ./minimap2 -x ava-pb reads.fa reads.fa > overlaps.paf # PacBio read overlap
./minimap2 -x ava-ont reads.fa reads.fa > overlaps.paf # Nanopore read overlap ./minimap2 -x ava-ont reads.fa reads.fa > overlaps.paf # Nanopore read overlap
@ -185,6 +186,19 @@ This is because SIRV does not honor the evolutionarily conservative splicing
signal. If you are studying SIRV, you may apply `--splice-flank=no` to let signal. If you are studying SIRV, you may apply `--splice-flank=no` to let
minimap2 only model GT..AG, ignoring the additional base. minimap2 only model GT..AG, ignoring the additional base.
Since v2.17, minimap2 can optionally take annotated genes as input and
prioritize on annotated splice junctions. To use this feature, you can
```sh
paftools.js gff2bed anno.gff > anno.bed
minimap2 -ax splice --junc-bed anno.bed ref.fa query.fa > aln.sam
```
Here, `anno.gff` is the gene annotation in the GTF or GFF3 format (`gff2bed`
automatically tests the format). The output of `gff2bed` is in the 12-column
BED format, or the BED12 format. With the `--junc-bed` option, minimap2 adds a
bonus score (tuned by `--junc-bonus`) if an aligned junction matches a junction
in the annotation. Option `--junc-bed` also takes 5-column BED, including the
strand field. In this case, each line indicates an oriented junction.
#### <a name="long-overlap"></a>Find overlaps between long reads #### <a name="long-overlap"></a>Find overlaps between long reads
```sh ```sh

2
minimap2.1
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@ -391,7 +391,7 @@ BED12 file can be converted from GTF/GFF3 with `paftools.js gff2bed anno.gtf'
.BR --junc-bonus \ INT .BR --junc-bonus \ INT
Score bonus for a splice donor or acceptor found in annotation (effective with Score bonus for a splice donor or acceptor found in annotation (effective with
.BR --junc-bed ) .BR --junc-bed )
[0]. [9].
.TP .TP
.BI --end-seed-pen \ INT .BI --end-seed-pen \ INT
Drop a terminal anchor if Drop a terminal anchor if