genomecov VS bamCoverage
0
0
Entering edit mode
10 months ago

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

coverage NGS PRO-seq • 501 views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 639 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6