computeMatrix in deeptool is Running with no result

Question

[adR]

Hi All, I wonder if someone can help me in explaining what to input on the -R <bed file> argument of the code below?

  computeMatrix scale-regions -S <bigwig file(s)> -R <bed file> -b 1000

what I did for example,

1. I download the Reference Genome Annotation file(GFF3 format )from https://www.ncbi.nlm.nih.gov/projects/genome/guide/human/index.shtml and saved it hg38.GFF3
2. Then, I converted the GFF3 to BED format and I saved it as hg38.bed
3. For -S argument I inserted the list of my bigwig files that I generate from bam files
4. Then I run the code below to generate the matrix

 computeMatrix scale-regions -S  3.bigwig  13.bigwig 19.bigwig  -R  hg38.bed   
-b 1000  -p 12 --outFileNameMatrix  matrix.mat.gz

I did not encounter errors but my machine is running since yesterday for almost 9 hrs and no result is produced. I would appreciate it if someone can comment on the input files.

Thank you!

[GenoMax]

As I recall it can take a long time for some of the deepTools tools. As long as the program is actually running i.e. you can see it using CPU cycles in top then you may need to be patient.

[adR]

GenoMax , Thanks a lot! I hope the code and the file hg38.bed are fine, right?

Answer 1

[sebastian.gregoricchio]

As GenoMax said, computeMatrix could take quite long. Especially if you run it all over the full genome and on an ordinary machine.

If you want just to check whether your code works well just try it on few regions. You can just filter your bed file by:

head -n 20 hg38.bed > hg38_n20.bed

Or just open your bed and take some rows and save it in a new bed file.