about how to use bamCoverage

Jiang Xu

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Oct 21, 2019, 5:04:38 PM10/21/19

to deepTools

Hey guys,

I am learning to use bamCoverage and found that the software ask for a index file in order for bamCoverage to do the work. But how to input the index file was not mentioned in the instructions. Is it by default to be the same folder, or the same folder and also with the same prefix as the bam file?

Thank you!

Best!

Jiang Xu

Lin Chen's Lab

Department of Biological Sciences, Computational and Molecular Biology

University of Southern California

Devon Ryan

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Oct 21, 2019, 5:10:47 PM10/21/19

to Jiang Xu, deepTools

Hi Jiang Xu,

BAM index files always have the same prefix and are in the same
program for all programs (be it deepTools or any other). Just run
`samtools index` on the file and you'll be good to go.

Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany

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Jiang Xu

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Oct 23, 2019, 2:33:05 PM10/23/19

to Devon Ryan, deepTools

Thanks a lot!

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