msauria
commented
4 years ago At first glance I'm not sure what the problem is. I've used your example matrix file and it works for me. The two things to pay attention to are 1) Do you get a message saying that is loading your matrix file(s)? This is unfortunately a little tricky to assess as the messages over-write each other as the program steps through each phase of the dataset creation. However, if you pipe the stderr into a file with hifive hic-data -X "test_*.MatA" out_filename.txt output.hic.data 2> hifive.log then you can look at the log file and see if each file name appears. If not, then there is an issue with the automatic recognition of the file names, which brings me to the second thing to check. 2) Do your chromosome names in the matrix file names match those in your fend.bed file? If your fend.bed chromosome names are 'chr1', 'chr2', etc, then your matrix file names need to be test_chr1.mat, test_chr2.mat, test_chr1_bychr2.mat and the argument you pass should be 'test*.mat'. If this isn't the issue, let me know and we can keep digging.
pubudumanoj
I tried to create a hic-data object using following commands
hifive fends -B fend.bed --binned=50000 out_filename.txt
When I run hifive hic-data -X "test_*.MatA" out_filename.txt output.hic.data I get "Done 0 cis reads, 0 trans reads" in the command line output and I cannot use this file for next steps (which is 6.4kb in size).
I obtained interaction matrices from homer and modified it according to the explanation in the documentation. My structure for one test_*.MatA file is chr1:0-50000 chr1:50000-100000 chr1:100000-150000 chr1:150000-200000 chr1:0-50000 7 0 0 0 chr1:50000-100000 0 11 0 0 chr1:100000-150000 0 0 28 0 chr1:150000-200000 0 0 0 0
The headers are column and row names and file is a TSV file
Can you please guide me how to resolve this issue or whether something wrong with my matrix structure