computeMatrix "Warning: Your chromosome names do not match..."

[samuelc...@gmail.com]

Hi,

I have an odd warning message running computeMatrix:

Warning: Your chromosome names do not match.
Please check that the chromosome names in your BED file
correspond to the names in your bigWig file.
An empty line will be added you your heatmap.
The offending chromosome name is chr5

I get a lot of these messages with different chromosome. However I am sure that my chromosome names are the same between my bed and my bigwig.

Checking the code, I found in hetmapper.py this:

# intialize values array. The length of the array
# is the length of the region which is defined
# by the start of the first zone zones[0][0]
# to the end of the last zone zones[-1][1]
valuesArray = np.zeros(zones[-1][1] - zones[0][0])
if not nansAsZeros:
valuesArray[:] = np.nan
try:
bw_array = bigwig.get_as_array(chrom,
max(0, zones[0][0]),
zones[-1][1])
# print chrom, zones[1]
# print bigwig.get_as_array(chrom, zones[1][0], zones[1][1])
except Exception as detail:
sys.stderr.write("Exception found. Message: "
"{}\n".format(detail))

if bw_array is None:
[...]
if bw_array is None:
sys.stderr.write("Warning: Your chromosome names do "
"not match.\nPlease check that the "
"chromosome names in your BED "
"file\ncorrespond to the names in your "
"bigWig file.\nAn empty line will be "
"added you your heatmap.\nThe offending "
"chromosome name is "
"{}\n\n".format(chrom))

Do you get a "None" only if the chromosome name does not match, or also there is no signal at all on all this region?
I made some quick test and it seems to me that it is the second, but I am not sure, because I could get some all 0 lines without warning...

[Fidel Ramirez]

Hi Samuel, 

Can you share privately one of the bigwig files with a problem together with the command line that you used. So far, I had only seen the 'None' problem for chromosome names that are not in the bigwig file but you may have a different case here. 

Best,

Fidel

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Fidel Ramirez