What's the meaning of HICCUPS result

liuzhe...@gmail.com

unread,

Nov 18, 2018, 8:18:58 AM11/18/18

to 3D Genomics

Dear all,

Thanks for involving this discussion.

When I am running hiccups using juicer tools by the following scripts,

java -jar juicer_tools.1.9.8_jcuda.0.8.jar hiccups --cpu s1_s2_s3.sort.hic HICCUP

I got several files:

enriched_pixels_10000.bedpe enriched_pixels_5000.bedpe fdr_thresholds_25000 merged_loops.bedpe postprocessed_pixels_25000.bedpe
enriched_pixels_25000.bedpe fdr_thresholds_10000 fdr_thresholds_5000 postprocessed_pixels_10000.bedpe postprocessed_pixels_5000.bedpe

Personally speaking, I think merged_loops.bedpe file is the loop file. But could you explain what the meaning of other 9 files?

It's filtered by FDR value? But I don't know what is the enriched_pixels or postprocessed_pixels?

Thanks for your kind answer.

Best wishes,

Zhe

liuzhe...@gmail.com

unread,

Nov 18, 2018, 8:21:22 AM11/18/18

to 3D Genomics

And if 5000, 10000, and 25000 represent for resolution, what's the resolution of merged_loops.bedpe?

在 2018年11月18日星期日 UTC+8下午9:18:58，liuzhe...@gmail.com写道：

Neva Durand

unread,

Nov 18, 2018, 3:15:57 PM11/18/18

to liuzhe...@gmail.com, 3d-ge...@googlegroups.com

Please look at the documentation here: https://github.com/aidenlab/juicer/wiki/HiCCUPS

And for further information, consult the supplementary materials here: http://www.cell.com/cell/abstract/S0092-8674(14)01497-4

--
You received this message because you are subscribed to the Google Groups "3D Genomics" group.
To unsubscribe from this group and stop receiving emails from it, send an email to 3d-genomics...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/6c82a619-16de-4ac2-978c-353dcbc69c25%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--

Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org

liufuy...@gmail.com

unread,

Nov 23, 2018, 7:39:15 AM11/23/18

to Neva Durand, liuzhe...@gmail.com, 3d-ge...@googlegroups.com

Dear Neva Durand,

I use hiccup call loops for normal and cancer tissues, and I get 11000 and 16000 loops respectivly. But I use hiccupdiff for compare, there are only ~1000 loops conserved. ls the results confident?Thank you!

---Original---

From: "Neva Durand"<ne...@broadinstitute.org>

Date: Mon, Nov 19, 2018 04:15 AM

To: "liuzhehayida"<liuzhe...@gmail.com>;

Cc: "3d-genomics"<3d-ge...@googlegroups.com>;

Subject: Re: What's the meaning of HICCUPS result

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/CAF1CciW65YM%3DdPq5d%2BdHZfyLoc2AF4COMzOX9z6o4ULhsKHGhg%40mail.gmail.com.

Muhammad Saad Shamim

unread,

Nov 23, 2018, 7:41:22 AM11/23/18

to 3d-ge...@googlegroups.com, liufuy...@gmail.com, ne...@broadinstitute.org, liuzhe...@gmail.com

Did you mean to say that HiCCUPSDiff calls only 1000 of them different?

- Muhammad Saad Shamim

On Fri, Nov 23, 2018 at 6:39 AM wrote:

Dear Neva Durand,
I use hiccup call loops for normal and cancer tissues, and I get 11000 and 16000 loops respectivly. But I use hiccupdiff for compare, there are only ~1000 loops conserved. ls the results confident?Thank you!

---Original---
From: "Neva Durand"<>

Date: Mon, Nov 19, 2018 04:15 AM

To: "liuzhehayida"<>;
Cc: "3d-genomics"<3>;

Subject: Re: What's the meaning of HICCUPS result

Please look at the documentation here: https://github.com/aidenlab/juicer/wiki/HiCCUPS

And for further information, consult the supplementary materials here: http://www.cell.com/cell/abstract/S0092-8674(14)01497-4

On Sun, Nov 18, 2018 at 8:21 AM <> wrote:

And if 5000, 10000, and 25000 represent for resolution, what's the resolution of merged_loops.bedpe?

在 2018年11月18日星期日 UTC+8下午9:18:58，写道：
Dear all,

Thanks for involving this discussion.
When I am running hiccups using juicer tools by the following scripts,

java -jar juicer_tools.1.9.8_jcuda.0.8.jar hiccups --cpu s1_s2_s3.sort.hic HICCUP

I got several files:

enriched_pixels_10000.bedpe enriched_pixels_5000.bedpe fdr_thresholds_25000 merged_loops.bedpe postprocessed_pixels_25000.bedpe
enriched_pixels_25000.bedpe fdr_thresholds_10000 fdr_thresholds_5000 postprocessed_pixels_10000.bedpe postprocessed_pixels_5000.bedpe

Personally speaking, I think merged_loops.bedpe file is the loop file. But could you explain what the meaning of other 9 files?
It's filtered by FDR value? But I don't know what is the enriched_pixels or postprocessed_pixels?

Thanks for your kind answer.

Best wishes,
Zhe

--
You received this message because you are subscribed to the Google Groups "3D Genomics" group.

To unsubscribe from this group and stop receiving emails from it, send an email to 3d-genomics+unsubscribe@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/6c82a619-16de-4ac2-978c-353dcbc69c25%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--
Neva Cherniavsky Durand, Ph.D.
Staff Scientist, Aiden Lab
www.aidenlab.org

--
You received this message because you are subscribed to the Google Groups "3D Genomics" group.

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/CAF1CciW65YM%3DdPq5d%2BdHZfyLoc2AF4COMzOX9z6o4ULhsKHGhg%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.

--

You received this message because you are subscribed to the Google Groups "3D Genomics" group.

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/5bf7e089.1c69fb81.c9c52.643b%40mx.google.com.

liufuy...@gmail.com

unread,

Nov 23, 2018, 7:47:16 AM11/23/18

to Muhammad Saad Shamim, 3d-ge...@googlegroups.com, liuzhe...@gmail.com, Neva Cherniavsky Durand

yes,a lot of is different

---Original---

From: "Muhammad Saad Shamim"<sa50...@gmail.com>

Date: Fri, Nov 23, 2018 20:41 PM

To: "liufuyan2018"<liufuy...@gmail.com>;

Cc: "3d-genomics"<3d-ge...@googlegroups.com>;"liuzhehayida"<liuzhe...@gmail.com>;"Neva Cherniavsky Durand"<ne...@broadinstitute.org>;

Subject: Re: What's the meaning of HICCUPS result

Hey Zhe,

Did you mean to say that HiCCUPSDiff calls only 1000 of them different?

- Muhammad Saad Shamim

On Fri, Nov 23, 2018 at 6:39 AM liufuy...@gmail.com <liufuy...@gmail.com> wrote:

Dear Neva Durand,
I use hiccup call loops for normal and cancer tissues, and I get 11000 and 16000 loops respectivly. But I use hiccupdiff for compare, there are only ~1000 loops conserved. ls the results confident?Thank you!

---Original---
From: "Neva Durand"<ne...@broadinstitute.org>

Date: Mon, Nov 19, 2018 04:15 AM

To: "liuzhehayida"<liuzhe...@gmail.com>;
Cc: "3d-genomics"<3d-ge...@googlegroups.com>;

Subject: Re: What's the meaning of HICCUPS result

Please look at the documentation here: https://github.com/aidenlab/juicer/wiki/HiCCUPS

And for further information, consult the supplementary materials here: http://www.cell.com/cell/abstract/S0092-8674(14)01497-4

On Sun, Nov 18, 2018 at 8:21 AM <liuzhe...@gmail.com> wrote:

And if 5000, 10000, and 25000 represent for resolution, what's the resolution of merged_loops.bedpe?

在 2018年11月18日星期日 UTC+8下午9:18:58，liuzhe...@gmail.com写道：

Dear all,

Thanks for involving this discussion.
When I am running hiccups using juicer tools by the following scripts,

java -jar juicer_tools.1.9.8_jcuda.0.8.jar hiccups --cpu s1_s2_s3.sort.hic HICCUP

I got several files:

enriched_pixels_10000.bedpe enriched_pixels_5000.bedpe fdr_thresholds_25000 merged_loops.bedpe postprocessed_pixels_25000.bedpe
enriched_pixels_25000.bedpe fdr_thresholds_10000 fdr_thresholds_5000 postprocessed_pixels_10000.bedpe postprocessed_pixels_5000.bedpe

Personally speaking, I think merged_loops.bedpe file is the loop file. But could you explain what the meaning of other 9 files?
It's filtered by FDR value? But I don't know what is the enriched_pixels or postprocessed_pixels?

Thanks for your kind answer.

Best wishes,
Zhe

--
You received this message because you are subscribed to the Google Groups "3D Genomics" group.

To unsubscribe from this group and stop receiving emails from it, send an email to 3d-genomics...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/6c82a619-16de-4ac2-978c-353dcbc69c25%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--
Neva Cherniavsky Durand, Ph.D.
Staff Scientist, Aiden Lab
www.aidenlab.org

--
You received this message because you are subscribed to the Google Groups "3D Genomics" group.

To unsubscribe from this group and stop receiving emails from it, send an email to 3d-genomics...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/CAF1CciW65YM%3DdPq5d%2BdHZfyLoc2AF4COMzOX9z6o4ULhsKHGhg%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.

--
You received this message because you are subscribed to the Google Groups "3D Genomics" group.

To unsubscribe from this group and stop receiving emails from it, send an email to 3d-genomics...@googlegroups.com.

Muhammad Saad Shamim

unread,

Nov 23, 2018, 7:50:41 AM11/23/18

to liufuy...@gmail.com, 3d-ge...@googlegroups.com, liuzhe...@gmail.com, Neva Cherniavsky Durand

What file is this number based off of?

HiCCUPSDiff creates 2 main files, listing loops unique to the first and second maps.

It doesn't directly list conserved loops per se.

- Muhammad Saad Shamim

On Fri, Nov 23, 2018 at 6:47 AM liufuy...@gmail.com <liufuy...@gmail.com> wrote:

yes,a lot of is different

---Original---
From: "Muhammad Saad Shamim"<sa50...@gmail.com>
Date: Fri, Nov 23, 2018 20:41 PM
To: "liufuyan2018"<liufuy...@gmail.com>;
Cc: "3d-genomics"<3d-ge...@googlegroups.com>;"liuzhehayida"<liuzhe...@gmail.com>;"Neva Cherniavsky Durand"<ne...@broadinstitute.org>;
Subject: Re: What's the meaning of HICCUPS result

liufuy...@gmail.com

unread,

Nov 23, 2018, 7:10:32 PM11/23/18

to Muhammad Saad Shamim, 3d-ge...@googlegroups.com, liuzhe...@gmail.com, Neva Cherniavsky Durand

I use( total number -both unique number)/2

---Original---

From: "Muhammad Saad Shamim"<sa50...@gmail.com>

Date: Fri, Nov 23, 2018 20:50 PM

Muhammad Saad Shamim

unread,

Nov 23, 2018, 7:14:57 PM11/23/18

to liufuy...@gmail.com, 3d-ge...@googlegroups.com, liuzhe...@gmail.com, Neva Cherniavsky Durand

did you run hiccups on the mapq 30 files?

- Muhammad Saad Shamim

liufuy...@gmail.com

unread,

Nov 23, 2018, 7:55:18 PM11/23/18

to Muhammad Saad Shamim, 3d-ge...@googlegroups.com, liuzhe...@gmail.com, Neva Cherniavsky Durand

use maq 20

---Original---

From: "Muhammad Saad Shamim"<sa50...@gmail.com>

Date: Sat, Nov 24, 2018 08:14 AM

Muhammad Saad Shamim

unread,

Nov 23, 2018, 8:36:22 PM11/23/18

to liufuy...@gmail.com, 3d-ge...@googlegroups.com

Do the loop calls seem appropriate/valid in juicebox? Ive never worked with map q20.

What resolutions did you run on? How many reads are in this map?

liufuy...@gmail.com

unread,

Nov 23, 2018, 9:29:08 PM11/23/18

to Muhammad Saad Shamim, 3d-ge...@googlegroups.com

normal tissues is ~10000,cancer tissues is ~16000,should I filter CNV region for calling loops?

---Original---

From: "Muhammad Saad Shamim"<sa50...@gmail.com>

Date: Sat, Nov 24, 2018 09:36 AM

To: "liufuyan2018"<liufuy...@gmail.com>;

Cc: "3d-genomics"<3d-ge...@googlegroups.com>;

Muhammad Saad Shamim

unread,

Nov 23, 2018, 9:59:22 PM11/23/18

to liufuy...@gmail.com, 3d-ge...@googlegroups.com

Do the loop calls look appropriate in Juicebox?

- Muhammad Saad Shamim

葉培民

unread,

Nov 25, 2018, 10:57:22 PM11/25/18

to Muhammad Saad Shamim, 3d-ge...@googlegroups.com, liufuy...@gmail.com

Muhammad Saad Shamim <sa50...@gmail.com>於 2018年11月24日週六，上午10:59寫道：

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/CAFrDNA%3DWw0D8CJpG0xr4HWNs9WbZ2Z_q_ye63Gjp9RbwFJAvCA%40mail.gmail.com.

liufuy...@gmail.com

unread,

Dec 1, 2018, 5:02:57 AM12/1/18

to Muhammad Saad Shamim, 3d-ge...@googlegroups.com

yes.should I filter CNV region for calling loops in cancer samples?

---Original---

From: "Muhammad Saad Shamim"<sa50...@gmail.com>

Date: Sat, Nov 24, 2018 10:59 AM

Reply all

Reply to author

Forward