Matt's Group-3

How to interpret genome dot plots (#dotplots #genomic).

How to do a dotplot with minimap2:

minimap2 -DP ref.fa query.fa|miniasm/minidot - > dot.eps

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