Can't find cooler file after loading in data

I used this command:

cooler load -f coo chromsizes.tsv:1 output.tsv matrix.cool --count-as-float

but afterwards no matrix.cool file appeared in my current directory or anywhere on my machine. Here is the file I tried to convert: output.tsv

Thanks in advance!

[nvictus]

It looks like there’s a mismatch between the matrix you’re asking for (1kb resolution) and the one you are providing… it looks like it might be restriction fragment-delimited? You would have to provide a bed file with the bin segmentation that was used.

If your goal was to aggregate that matrix to 1kb, then try cooler cload pairs:

cooler cload pairs \
    --assembly dm6 \
    --tril-action drop \
    -c1 1 -p1 2 -c2 4 -p2 5 \
    --field count,7,float,sum \
    dm6.chrom.sizes:1000 matrix.bg2.gz matrix.1000.cool 

I used the following chrom sizes and it worked:

2L	23513712
2R	25286936
3L	28110227
3R	32079331
4	1348131
X	23542271
Y	3667352

[daniellenguyen]

Thank you!