Hi I have a silly question: What is the difference between samtools depth and bedtools genomecov? For both tools, the input file needs to be *.sorted.bam, which was generated by sam->bam->sorted.bam.
I tried both tools using the same *.sorted.bam input file and they generate the same coverage file.
Can I use bedtools to map reads file (fastq or fasta ) to a reference genome? Like bowtie or bwa did? Because I like the function of bedtools that gives you how many reads map to the genome, and also the percentage of genome that is mapped by the reads.