genomecov VS bamCoverage

Question

[c.heininger]

Hello,

can someone help me understand the differences between bedtools' genomecov and deepTools' bamCoverage? Are they used interchangeably, are there key differences, can I generate the same results with both tools? I have sequencing data from a paired-end PRO-seq experiment and for generating the coverage tracks I am not sure which tool to "trust", as I have not been able to reproduce their respective results with each other.

Any experience, thoughts, directions? I am grateful for any input!

Cheers

[Marco Pannone]

If you need to visualize your data in a Genome Browser (such as IGV or UCSC) I would suggest you go with bamCoverage. I have never used genomecov but I never had problems in using bamCoverage.

[Friederike]

I have not been able to reproduce their respective results with each other

Did you use a scaling factor with genomecov? What was the bin size you used for bamCoverage? Unless you share both lines of codes it's difficult to help you pin point the issue. Apart from the two factors "scaling" and "bin size", there are more details that may differ, such as the counting of fragments rather than reads for paired-end data.