O/E data not available

[YuhaoDoong]

Hi I had a problem when I was running juicer box dump from HiC data which contain 180M validpairs. However, it showed "O/E data not available at chr5 BP_25000 KR", and could not generate results file. But when I extracted only 10M validpairs, it worked well. May I ask, what should I do to get whole data dump file ?

The code ran as " ~/HiC-Pro_2.11.4/bin/utils/hicpro2juicebox.sh -i 2221-1.hicup.180M.validPairs -g mm10 -j ~/juicer_tools_1.22.01.jar -r ~/HiC-Pro_2.11.4/annotation/MboI_mm10.bed -o ./"

And it reported as "WARN [2021-03-08T14:11:31,075] [Globals.java:138] [main] Development mode is e nabled O/E data not available at chr5 BP_25000 KR"

Have a nice day. Best Yuhao

[nchernia]

Hello

It is possible there is no data at 25Kb normalized at KR. Try using SCALE, our updated balancing normalization (and use Juicer Tools during pre to ensure that SCALE is included).

On Mon, Mar 8, 2021 at 2:44 AM Stormsky99 notifications@github.com wrote:

Hi I had a problem when I was running juicer box dump from HiC data which contain 180M validpairs. However, it showed "O/E data not available at chr5 BP_25000 KR", and could not generate results file. But when I extracted only 10M validpairs, it worked well. May I ask, what should I do to get whole data dump file ?

The code ran as " ~/HiC-Pro_2.11.4/bin/utils/hicpro2juicebox.sh -i 2221-1.hicup.180M.validPairs -g mm10 -j ~/juicer_tools_1.22.01.jar -r ~/HiC-Pro_2.11.4/annotation/MboI_mm10.bed -o ./"

And it reported as "WARN [2021-03-08T14:11:31,075] [Globals.java:138] [main] Development mode is e nabled O/E data not available at chr5 BP_25000 KR"

Have a nice day. Best Yuhao

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-- Neva Cherniavsky Durand, Ph.D. | she, her, hers Assistant Professor | Molecular and Human Genetics Aiden Lab | Baylor College of Medicine www.aidenlab.org

[YuhaoDoong]

Hi, Thank you for reply. But I still can not extract data from any normalization. And in JuicerBox visualization, I can't choose any normalization either.

My hic file was generated from HiC-Pro validpairs, and with less validpairs, Juicer_tools worked well.

May Juicer_tools be not compatible with high validpairs HiC-Pro data?

[nchernia]

You cannot choose any normalization at any resolution?

On Tue, Mar 23, 2021 at 2:52 AM Stormsky99 @.***> wrote:

Hi, Thank you for reply. But I still can not extract data from any normalization. And in JuicerBox visualization, I can't choose any normalization either.

My hic file was generated from HiC-Pro validpairs, and with less validpairs, Juicer_tools worked well.

May Juicer_tools be not compatible with high validpairs HiC-Pro data?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/aidenlab/juicer/issues/209#issuecomment-804664050, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAK2EW2Z47P2TJZRM2ND5DDTFA3AHANCNFSM4YY4QLRA .

-- Neva Cherniavsky Durand, Ph.D. | she, her, hers Assistant Professor | Molecular and Human Genetics Aiden Lab | Baylor College of Medicine www.aidenlab.org

[YuhaoDoong]

Yes, all normalization at any resolution in "JuicerBox" and "juicer_tools dump" were failed with hic file which was generated from 180,000,000 validpairs. Only "NONE" could be chosen. But when I generate hic file with half validpairs, 90,000,000, the normalization worked well. It's so confused. Perhaps, there were some problems in the codes I ran? Or juicer_tools is not compatible with too much validpairs from HiC-Pro?

hicpro2juicebox.sh -i hicup.180M.validPairs -g mm10 -j juicer_tools_1.22.01.jar -r MboI_mm10.bed -o ./ hicpro2juicebox.sh -i hicup.90M.validPairs -g mm10 -j juicer_tools_1.22.01.jar -r MboI_mm10.bed -o ./

java -jar juicer_tools_1.22.01.jar dump oe KR hicup.180M.validPairs.hic chr1 chr2 BP 25000 test.txt java -jar juicer_tools_1.22.01.jar dump oe KR hicup.90M.validPairs.hic chr1 chr2 BP 25000 test.txt

Best

[nchernia]

If your hic file is loading, you can just run addNorm on it.

https://github.com/aidenlab/juicer/wiki/AddNorm

On Tue, Mar 23, 2021 at 7:11 AM Stormsky99 @.***> wrote:

Yes, all normalization at any resolution in "JuicerBox" and "juicer_tools dump" were failed with hic file which was generated from 180,000,000 validpairs. Only "NONE" could be chosen. But when I generate hic file with half validpairs, 90,000,000, the normalization worked well. It's so confused. Perhaps, there were some problems in the codes I ran? Or juicer_tools is not compatible with too much validpairs from HiC-Pro?

hicpro2juicebox.sh -i hicup.180M.validPairs -g mm10 -j juicer_tools_1.22.01.jar -r MboI_mm10.bed -o ./ hicpro2juicebox.sh -i hicup.90M.validPairs -g mm10 -j juicer_tools_1.22.01.jar -r MboI_mm10.bed -o ./

java -jar juicer_tools_1.22.01.jar dump oe KR hicup.180M.validPairs.hic chr1 chr2 BP 25000 test.txt java -jar juicer_tools_1.22.01.jar dump oe KR hicup.90M.validPairs.hic chr1 chr2 BP 25000 test.txt

Best

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-- Neva Cherniavsky Durand, Ph.D. | she, her, hers Assistant Professor | Molecular and Human Genetics Aiden Lab | Baylor College of Medicine www.aidenlab.org