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aidenlab / straw

Extract data quickly from Juicebox via straw
MIT License
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Error finding block data #123

Open DavidWarrenKatz opened 1 year ago

DavidWarrenKatz commented 1 year ago

Often, when calling the getMatrixZoomData function, I receive an "Error finding block data" error. For example, the following code produces the error:

import hicstraw hic = hicstraw.HiCFile("https://www.encodeproject.org/files/ENCFF247KEK/@@download/ENCFF247KEK.hic")

resolution = 5000; chromosome = '1'; startingbp = 10000000; endingbp = 13000000;

matrix_object_chr1 = hic.getMatrixZoomData(chromosome, chromosome, "observed", "NONE", "BP", resolution)

sa501428 commented 1 year ago

Have you tried with 'chr1' instead of '1'? The chromosome depends on the chrom.sizes file specified.

DavidWarrenKatz commented 1 year ago

Thank you.

DavidWarrenKatz commented 1 year ago

where is the chrome.sizes file located? I am pretty sure the name of the chromosomes is correct, as it matches what is output for hic.getChromosomes()[1].name. However, I am now receiving the error "Remote file doesn't have the given chr_chr map", but the map I am requesting for sure exists.

danidigi commented 2 months ago

Hi, I get the same errors when I try to use a .hic file as input for fithichip. Did you find a solution? Thank you ;)