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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
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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