mapping-reads-for-ORF-coverage.md

All reads and MAGs are origin from JGI

https://img.jgi.doe.gov/cgi-bin/mer/main.cgi?section=MetagenomeBins&page=metagenomeBins&taxon_oid=3300056388&dbtype=bin

Mapped reads with bowtie to each MAG and sorted the resulting SAM file

bowtie2 -x [metagenome] –interleaved [MAG] -S [metagenome.MAG.sam] samtools view -bS [SAM FILE] | samtools sort -@ 4 -o [SAM FILE sorted]

HT-seq estimated read coverage of each ORF

htseq-count -t CDS -i ID -f [sam] [MAG.gff] > [MAG.htseq]