straw: rapidly stream data from .hic files
Straw is library which allows rapid streaming of contact data from .hic files.
References:
- Neva C. Durand, James T. Robinson, Muhammad S. Shamim, Ido Machol, Jill P. Mesirov,
Eric S. Lander, and Erez Lieberman Aiden1
Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom.
Cell Systems 3 (2016), 99–101
DOI: 10.1016/j.cels.2015.07.012
Documentation
Important Notes
- Module Name: straw (see the modules page for more information)
- Unusual environment variables set
- STRAW_HOME installation directory
- STRAW_BIN executable directory
- STRAW_DATA sample data directory
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive
[user@cn3144 ~]$ module load straw
[+] Loading singularity 3.10.5 on cn4172
[+] Loading straw 1.3.1
The straw application installed on Biowulf comprises the R and Python versions.
The basdic usage of the R version is as follows:
[user@cn3144 ~]$ R
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
...
> library(strawr)
> library(mariner)
>
...
To use the Python version, type:
[user@cn3144 ~]$ python
Python 3.10.9 (main, Mar 8 2023, 10:47:38) [GCC 11.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import hicstraw
>>> import mustache
>>>
...
End the interactive session:
[user@cn3111 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$