Re: Usage of addNorm for multiple resolutions

[Muhammad Shamim]

Answered on other thread; just don't specify the resolution/r flag and it will be computed for all resolutions.

On Tuesday, May 10, 2022 at 4:30:38 AM UTC-5 huoyub...@gmail.com wrote:

Hi,

I am using .hic files from 4DN which were generated by Juicer Tools (version 1.8.9-cuda8) and contained VC, VC_SQRT, KR normalizations as stated in their pipeline (https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline). 

As suggested by many others, SCALE performs better than KR in most cases, so I want to use addNorm to add the SCALE normalizations. When I check the usage using the command "java -jar juicer_tools_1.22.01.jar addNorm", it shows:

Usage:   juicer_tools addNorm <input_HiC_file> [input_vector_file]
           : -d use intra chromosome (diagonal) [false]
           : -F don't calculate normalization for fragment-delimited maps [false]
           : -w <int> calculate genome-wide resolution on all resolutions >= input resolution [not set]
 Above options ignored if input_vector_file present
           : -k normalizations to include
           : -r resolutions for respective normalizations to build to
           : -j number of CPU threads to use

Then I tried the command "java -Xmx300G -jar juicer_tools_1.22.01 addNorm -d -F -k KR,VC_SQRT,SCALE -w 10000 -r 10000,10000,10000 -j 40 $hicfile"

and after dump I could get 10kb contacts with SCALE, VC_SQRT or KR, but not other resolutions such as 50kb with any normalization methods.

My question is how could I get the contacts at multiple resolutions?

I tried the command "java -Xmx300G -jar juicer_tools_1.22.01 addNorm -d -F -k SCALE,SCALE -w 50000 -r 100000,50000 -j 40 $hicfile"

and only get 50kb but not 100kb contacts after dump.

I also tried the command "java -Xmx300G -jar juicer_tools_1.22.01 addNorm -d -F -k SCALE,SCALE -w 50000 -r 50000,100000 -j 40 $hicfile"

and only get 100kb but not 50kb contacts after dump.

Is it because the addNorm only considers the last resolution for the normalization method? Then can I get multiple resolutions for the same normalization method? And how shall I know which resolution(s) I have in the .hic files?

Many thanks for any help in advance!

Kelly