Adding gene file to HiCPlotter "missing values" issue

[awezmm]

I input a triple sparse matrix as my hic file data. However that triple sparse matrix file represents a specific part in the genome. I then try to use -g flag to add my bed file with gene locations and I get the error:

Gene File (mm9-7-12-2016.bed) has some missing values

The bed file has locations of genes throughout the whole genome. However, my sparse matrix file has hic data only for a specific area in the the genome at a certain resolution. I extract my sparse file data using the straw program provided here: https://github.com/aidenlab/straw/wiki/CPP

I also use the -s and -e flags to match the same start and end positions.

Is the discrepancy in locations between the bed file and the sparse file the reason I am getting the error, and is there any way around it?

Thanks

[akdemirlab]

Hi,

I think it's most likely there are no genes within genomic region determined with the -s and -e parameter. I would change those parameters to see if it's the case. Otherwise, the chromosome names within your gene file might not be matching with the sparse matrix file.

Best - kadir

[EGeorgia]

Hello,

I am also having the same problem (again with a sorted mm9 bedfile) I have altered my -s and -e parameters but still get the same error message. I have tried with your data/hg19.RefSeq.sorted.bed and this works fine.

Is there anything else I could try to make this work?

Best,
Emily

[akdemirlab]

Hi Emily,

Chromosome names should start with "chr" in the bedGraph files such as chr1,chr2 instead of 1,2,3,...,X. Can you check if that's the issue with your mm9 file?
If not, please copy some parts of your file so I'll try to see if the issue is with something else.

Best - Kadir

[EGeorgia]

Hi Kadir,

Thanks for getting back to me. Yes I have that column in the correct format, I've attached my file - if you could have a look for me that would be great!

Many thanks,
Emily

mm9_genes_sorted3.bed.gz

[akdemirlab]

Hi Emily,

Your file seems fine - I couldnt find any formatting difference between it and data/hg19.RefSeq.sorted.bed file.
Just to be sure: do you have the right resolution or if you remove -s and -e parameters, do you still experience the problem?

I can try to assist further if you copy an example of none-working commands.

Best - Kadir