determining read-depth of given size of genomic window via samtools

Question

[ella]

Hi everyone :) I'm new in the field of bioinformatics and NGS analysis and would be glad if someone could help me. I want to compare read-depths of different samples along the genome (E.coli so no chromosomes). To do so, I would like to generate a table, in which the read depths of genomic windows of e.g. 100 nucleotides are listed (Pos. 1-100, 101-200, 201-300 and so on). I found, that samtools depth can give the coverage for each single nucleotide position. Is there the possibility, to adjust the output to my needs? Else, is there an easy-to-use linux command to convert a depth-per-nucleotide samtools output file into a depth-per-100ntwindow file? Thanks a lot in advance and have a nice day/ evening/.. :)

Answer 1

[GenoMax]

Take a look at bedtools genomecov (LINK).