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  • RE: How to...

    How to do a dotplot with minimap2:

    minimap2 -DP ref.fa query.fa|miniasm/minidot - > dot.eps
    
    posted in Matt
  • RE: How to...

    How to convert a minimap2 alignment to gff/gtf:
    https://github.com/lh3/minimap2/issues/455
    https://github.com/lh3/minimap2/files/9591008/bam2gff_fixGffread.zip
    bam2gff_fixGffread.zip

    minimap2 -t 10 -ax splice:hq -uf ref.fa cdna.fa |/Bio/bin/samtools-1.14 view -b > minimap2.tr.bam
    perl bam2gff.pl -b minimap2.tr.bam -o minimap2.tr.gff -s /Bio/bin/samtools-1.14 gffread minimap2.tr.gff -T -o minimap2.tr.gtf
    perl fixGffread.pl -i minimap2.tr.gtf -o minimap2.tr.fix.gtf
    

    Alternative method:

    #Align sequences and convert to BAM
    minimap2 -ax splice --cs target.fa query.fa | samtools sort -O BAM - > alignments.bam
    #Convert to BED12 using BEDtools
    bedtools bamtobed -bed12 -i alignments.bam > alignments.bed 
    #Convert to genePred using UCSC tools
    bedToGenePred alignments.bed alignments.genepred
    #Convert to GTF2 using UCSC tools. genePredToGtf has additional options that might be useful in specific use cases.
    genePredToGtf "file" alignments.genepred alignments.gtf
    
    posted in Matt