# from Miten:
# I downloaded the fastq file from https://osf.io/8f6n9/
# went to folder 20200302.... and download file IVT1.fastq.zst
# extract and replace Us with Ts in the fastq (!)
# align to genome with minimap2 -ax map-ont
# Make bam using samtools
# I got this BAM file from Miten:
wget http://public.gi.ucsc.edu/~miten/covid-19/IVT.sorted.bam
wget http://public.gi.ucsc.edu/~miten/covid-19/IVT.sorted.bam.bai
# sigh... need to change chrom name for UCSC
samtools view -h IVT.sorted.bam | sed -e 's/NC_045512.2/NC_045512v2/' | samtools view -Sb > IVT.ucsc.s.bam
samtools index IVT.ucsc.s.bam
bamCoverage -b IVT.ucsc.s.bam -o IVT.bw --binSize=1 -p 8
ln -s `pwd`/IVT.bw /gbdb/wuhCor1/bbi/IVT.bw