Groups

ngsplot-discuss

1–30 of 348

Welcome to the discussion group of ngs.plot - the coolest NGS plotting tool!

0 selected

Li Shen, … MikeD11

8/11/15

[Please contribute] Studies that cite ngs.plot

Dear Li Shen I recently cited your excellent software in the supplemental methods section of Josling

unread,

[Please contribute] Studies that cite ngs.plot

Dear Li Shen I recently cited your excellent software in the supplemental methods section of Josling

8/11/15

4/8/15

ngs.plot has migrated to Github!

The new address is here: https://github.com/shenlab-sinai/ngsplot The original Google code site has

unread,

ngs.plot has migrated to Github!

The new address is here: https://github.com/shenlab-sinai/ngsplot The original Google code site has

4/8/15

Li Shen, … Bing Yao3

4/25/14

ngs.plot manuscript has been published!

Congratulations! On Tuesday, April 15, 2014 10:22:04 AM UTC-4, Li Shen wrote: We are happy to

unread,

ngs.plot manuscript has been published!

Congratulations! On Tuesday, April 15, 2014 10:22:04 AM UTC-4, Li Shen wrote: We are happy to

4/25/14

Mark Rassner, Dahun2

10/30/25

I'm not a developer but I can suggest some tips for your problem. I think you should check your

unread,

I'm not a developer but I can suggest some tips for your problem. I think you should check your

10/30/25

Raphael, Sarah Muniz Nardeli2

12/4/23

Sense and antisense metaplot

Hi Rafael, Did you solve the sense/antisense metaplot issue? After a few testes, I am not even sure

unread,

Sense and antisense metaplot

Hi Rafael, Did you solve the sense/antisense metaplot issue? After a few testes, I am not even sure

12/4/23

Hongliang Zhang

8/15/23

Request for mm39 genome

Dear Li Shen, Would it be possible to add the mm39 genome to the reference database? I have mapped my

unread,

Request for mm39 genome

Dear Li Shen, Would it be possible to add the mm39 genome to the reference database? I have mapped my

8/15/23

6/16/23

Python 3 update for ngs.plot is available

Hello all, We had an individual question regarding if there is a tar package available for the Python

unread,

Python 3 update for ngs.plot is available

Hello all, We had an individual question regarding if there is a tar package available for the Python

6/16/23

Magda Maslon, Clayton Collings3

7/27/22

cnt file - library size

Thank you for your response. This is helpful, especially re .cnt file localization - I was trying to

unread,

cnt file - library size

Thank you for your response. This is helpful, especially re .cnt file localization - I was trying to

7/27/22

6/4/22

What kind of normalization to do when plotting aggragate plot using two different chip-seq bam files

Hi, all, I have two samples of Chip-seq experiment, one treated with DMSO and another treated with a

unread,

What kind of normalization to do when plotting aggragate plot using two different chip-seq bam files

Hi, all, I have two samples of Chip-seq experiment, one treated with DMSO and another treated with a

6/4/22

3/17/22

the locational information of the DNA sorted in the heatmap

Hello, I'm making ChIP-seq heatmap and trying to extract the sorted DNA information in the

unread,

the locational information of the DNA sorted in the heatmap

Hello, I'm making ChIP-seq heatmap and trying to extract the sorted DNA information in the

3/17/22

2/21/22

Which columns precisely correspond to the interval?

Which columns precisely in hm1.txt (from bin 1..101) have the values of the interval, and which have

unread,

Which columns precisely correspond to the interval?

Which columns precisely in hm1.txt (from bin 1..101) have the values of the interval, and which have

2/21/22

10/3/21

Problem installing genome: Disk quota exceeded

Hi all, I tried to install the enhancer by using: ngsplotdb.py install ngsplotdb_hg19_75_3.

unread,

Problem installing genome: Disk quota exceeded

Hi all, I tried to install the enhancer by using: ngsplotdb.py install ngsplotdb_hg19_75_3.

10/3/21

8/27/21

About the genes consideration

I wanted use all genes present in the db to get my enrichment plot but ngs.plot.r loading only

unread,

About the genes consideration

I wanted use all genes present in the db to get my enrichment plot but ngs.plot.r loading only

8/27/21

russell....@gmail.com

8/19/21

error in ngs.plot.r

Trying to conduct ngs.plot for ATACseq reads to create a TSS metaplot. Reaching the same error

unread,

error in ngs.plot.r

Trying to conduct ngs.plot for ATACseq reads to create a TSS metaplot. Reaching the same error

8/19/21

8/19/21

How NGS plot averages the gene list provided by the user

Hello Thanks for the tool my question is I have gene list which am providing, while averaging it will

unread,

How NGS plot averages the gene list provided by the user

Hello Thanks for the tool my question is I have gene list which am providing, while averaging it will

8/19/21

Q Ngo, … etiennedanis3

7/10/21

Request for hg38 genome

Hi Veena, I don't know if you already got a response fron Li Shen but the hg38 database already

unread,

Request for hg38 genome

Hi Veena, I don't know if you already got a response fron Li Shen but the hg38 database already

7/10/21

6/4/21

question about '-FL(fragment length)' option

Hello all! I have one question about fragment length of average plot. Actually, it is proper to set

unread,

question about '-FL(fragment length)' option

Hello all! I have one question about fragment length of average plot. Actually, it is proper to set

6/4/21

5/24/21

Reads Extraction

I generated a heatmap through ngsplot for three different samples. Now I want to pull out the reads

unread,

Reads Extraction

I generated a heatmap through ngsplot for three different samples. Now I want to pull out the reads

5/24/21

Clayton Collings2

5/17/21

Request for Chlorocebus_sabeus (African Green Monkey) - Available at UCSC

PS There is only one genome at UCSC for this genome, chlSab2. On Monday, May 17, 2021 at 2:20:01 AM

unread,

Request for Chlorocebus_sabeus (African Green Monkey) - Available at UCSC

PS There is only one genome at UCSC for this genome, chlSab2. On Monday, May 17, 2021 at 2:20:01 AM

5/17/21

11/17/20

Fragment length

Hi, 1) I want to see how peaks from macs2 (converted to BAM via bedtobam) are located relative to the

unread,

Fragment length

Hi, 1) I want to see how peaks from macs2 (converted to BAM via bedtobam) are located relative to the

11/17/20

11/9/20

Heatmap gene order error of TSS mode and signal disappearing

Hello everyone, I'm using ngsplot to draw many NGS data(ChIP-seq, RNA-seq and so on). When I was

unread,

Heatmap gene order error of TSS mode and signal disappearing

Hello everyone, I'm using ngsplot to draw many NGS data(ChIP-seq, RNA-seq and so on). When I was

11/9/20

Gepoliano Chaves

9/20/20

Enhancer Flag vs. TSS or genebody Flag

Hi all, I am new to ngsplots. I am trying to get a sense of peaks in the enhancer regions of my 5hmC

unread,

Enhancer Flag vs. TSS or genebody Flag

Hi all, I am new to ngsplots. I am trying to get a sense of peaks in the enhancer regions of my 5hmC

9/20/20

7/20/20

Single column heat map for TSS, genes appear out of order.

Hello Groups, I am using ngs.plot to show some transcription factor chip data, and the regions on my

unread,

Single column heat map for TSS, genes appear out of order.

Hello Groups, I am using ngs.plot to show some transcription factor chip data, and the regions on my

7/20/20

7/19/20

ngs.plot.r gives flat graphs and no results

Hi, I am running nags.plot.r on my indexed bam files for ChIP-seq data, however the output graphs are

unread,

ngs.plot.r gives flat graphs and no results

Hi, I am running nags.plot.r on my indexed bam files for ChIP-seq data, however the output graphs are

7/19/20

Xavi Sole, … Raphael6

7/14/20

Profiles stratified by strand

Hi all, This is a quite old trend. But did the situation change? Is it possible now to plot it on a

unread,

Profiles stratified by strand

Hi all, This is a quite old trend. But did the situation change? Is it possible now to plot it on a

7/14/20

Yoshihiro, Etienne Danis2

6/5/20

Flat plot without any error message

Hi Yoshihiro, It could be an issue with the config files. I would create the config file for one TF

unread,

Flat plot without any error message

Hi Yoshihiro, It could be an issue with the config files. I would create the config file for one TF

6/5/20

Déborah Manza Mianza

2/18/20

Request your reference genome here!

Sorry to bother you. I don't know if you still do that. But I'ld like if possible, to ask you

unread,

Request your reference genome here!

Sorry to bother you. I don't know if you still do that. But I'ld like if possible, to ask you

2/18/20

Sai Mukund Ramakrishnan

2/11/20

Issues when using default bed file

I uploaded my inputs to google drive. https://drive.google.com/drive/folders/

unread,

Issues when using default bed file

I uploaded my inputs to google drive. https://drive.google.com/drive/folders/

2/11/20

Margaret Walton, 胡新蕾2

2/11/20

ngsplot draw multiple average profile

Hi, I wonder if you have solved this problem? I have two groups of some data, one group is healthy

unread,

ngsplot draw multiple average profile

Hi, I wonder if you have solved this problem? I have two groups of some data, one group is healthy

2/11/20

Déborah Manza Mianza

1/27/20

request melon genome

Sorry to bother you. I don't know if you still do that. But I'ld like if possible, to ask you

unread,

request melon genome

Sorry to bother you. I don't know if you still do that. But I'ld like if possible, to ask you

1/27/20

1/8/20

Definition of 5' - 3' region in the case of BED file with locations of varying length

Hello, I am plotting (multiple) files using locations from a bed file.The locations in the bed file

unread,

Definition of 5' - 3' region in the case of BED file with locations of varying length

Hello, I am plotting (multiple) files using locations from a bed file.The locations in the bed file

1/8/20

Hua Li, … Shmuel Ruppo5

1/7/20

I have found the answer myself, so I am posting it here. In the case of the default algorithm (total)

unread,

I have found the answer myself, so I am posting it here. In the case of the default algorithm (total)

1/7/20

12/15/19

task 1 failed - "missing value where TRUE/FALSE needed"

There are a few lines of my BAM file including header. I think maybe there are some problems in this

unread,

task 1 failed - "missing value where TRUE/FALSE needed"

There are a few lines of my BAM file including header. I think maybe there are some problems in this

12/15/19

Search

Clear search

Close search

Google apps

Main menu