multiBamSummary, what it calculate?
when I use multiBamSummary bins , I don't kown how it calculates. To be specific, when I use the --outRawCounts , I get the output looks like :
chr6 11620 21620 285.0 297.0 321.0
chr6 21620 31620 373.0 274.0 316.0
I know that "bins mode" will split the genome into bins , but I don't know, for example, does the number 285.0 above mean that 285 reads have landed in the bin 116220-21620? And , Whether to use the center position of a read when determining which bin a read falls in ?
Thanks for your attention.
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1 answer
It's the coverage for the particular bam in that bin, in your case you had three bams so you get three columns in that file next to the coordinates, see https://deeptools.readthedocs.io/en/develop/content/tools/multiBamSummary.html#example
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