Cistrome

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Feb 9

Need ASPERA Help

Need to upload large files. Requires ASPERA Solutions. Please help.

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Need ASPERA Help

Need to upload large files. Requires ASPERA Solutions. Please help.

Feb 9

2/28/22

Hi, I would like to run the seqpostool and ceas analysis in cistrome. I have aligned all data to mm39

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Hi, I would like to run the seqpostool and ceas analysis in cistrome. I have aligned all data to mm39

2/28/22

qin.zhan...@gmail.com

5/21/21

is there output file for the result of peak annotation from CEAS ?

Hello, I am using CEAS to annotate my chipseq peaks. There are 3 output files i get after running, 1

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is there output file for the result of peak annotation from CEAS ?

Hello, I am using CEAS to annotate my chipseq peaks. There are 3 output files i get after running, 1

5/21/21

mij...@broadinstitute.org, beta-user2

10/28/20

BETA-plus error: ValueError: max() arg is an empty sequence

Did you solve the problem? 在2019年1月22日星期二 UTC 下午9:02:17<MK> 写道： I have been trying to get BETA-

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BETA-plus error: ValueError: max() arg is an empty sequence

Did you solve the problem? 在2019年1月22日星期二 UTC 下午9:02:17<MK> 写道： I have been trying to get BETA-

10/28/20

astou...@googlemail.com

9/17/20

BETA Error using data from not listed genome

Hello, I am running BETA locally and using a bed file and expression file for Bos Taurus. As advised

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BETA Error using data from not listed genome

Hello, I am running BETA locally and using a bed file and expression file for Bos Taurus. As advised

9/17/20

Ester Feldmesser

8/20/20

account deleted

Dear cistrome people, My account has been deleted and I would like to use it again. I wrote to '

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account deleted

Dear cistrome people, My account has been deleted and I would like to use it again. I wrote to '

8/20/20

8/8/20

OUtput result wrong

Hello, I have used BETA for analysis of plant species. BETA run successfully but problem is that

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OUtput result wrong

Hello, I have used BETA for analysis of plant species. BETA run successfully but problem is that

8/8/20

Jian Ma, Roberto Ferrari2

4/10/20

Re: BETA Basic error after "Genes were seprated to two parts: up regulated and down regulated."

same error here on terminal when i added my peaks of CTCF: Roberto:HAPRBs RobertoFerrari$ BETA plus -

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Re: BETA Basic error after "Genes were seprated to two parts: up regulated and down regulated."

same error here on terminal when i added my peaks of CTCF: Roberto:HAPRBs RobertoFerrari$ BETA plus -

4/10/20

4/8/20

"Heatmap" in Cistrome

Hi, I was trying to make a heatmap using "Heatmap" in Cistrome. Even I did "Run this

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"Heatmap" in Cistrome

Hi, I was trying to make a heatmap using "Heatmap" in Cistrome. Even I did "Run this

4/8/20

sajjad khani, … Roberto Ferrari6

4/8/20

BETA problem with format of diffrential gene expression data

same problem here with BETA 1.07 command: BETA basic -p high_accessibility.bed -e

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BETA problem with format of diffrential gene expression data

same problem here with BETA 1.07 command: BETA basic -p high_accessibility.bed -e

4/8/20

hy gg, Roberto Ferrari2

4/8/20

cistrome "Internal Server Error"

same problem here

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cistrome "Internal Server Error"

same problem here

4/8/20

doanduy...@gmail.com, … Calvin Tsang4

3/31/20

mm10 for running CEAS locally!

Dear Jian, I came across your post. I am also trying to download the mm10.refGene sqlite3 file to my

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mm10 for running CEAS locally!

Dear Jian, I came across your post. I am also trying to download the mm10.refGene sqlite3 file to my

3/31/20

PaulG, … Jian Ma14

3/4/20

hg38 refGene file for CEAS

Hi Qin, Please download from here. https://drive.google.com/drive/folders/

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hg38 refGene file for CEAS

Hi Qin, Please download from here. https://drive.google.com/drive/folders/

3/4/20

2/4/20

Hi Anyone know where I can download mm10.refGene for CEAS Thank you Samah

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Hi Anyone know where I can download mm10.refGene for CEAS Thank you Samah

2/4/20

Wenduo Ye, … Delara Saberan-Djoneidi5

1/16/20

BETA on cistrome galaxy not working

Hi Jian I have the similar problem using BETA toom on Cistrome, I used refseq genes, tried with mm9

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BETA on cistrome galaxy not working

Hi Jian I have the similar problem using BETA toom on Cistrome, I used refseq genes, tried with mm9

1/16/20

8/28/19

Error in visualizing data in UCSC Genome Browser

Hi - Some files are having an issue moving from the cistromeDB to UCSC through the click through,

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Error in visualizing data in UCSC Genome Browser

Hi - Some files are having an issue moving from the cistromeDB to UCSC through the click through,

8/28/19

Scientist Stacey, Jian Ma2

7/28/19

Not able to upload bed files

Hi, Cistrome AP is online and upload function is fixed. The BETA functions are also work now, somehow

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Not able to upload bed files

Hi, Cistrome AP is online and upload function is fixed. The BETA functions are also work now, somehow

7/28/19

Daria Der, Ricardo Linares2

7/9/19

Time Out error while dowloading BED Peaks

I experience the same issue... On Friday, April 26, 2019 at 5:33:07 AM UTC-4, Daria Der wrote: I

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Time Out error while dowloading BED Peaks

I experience the same issue... On Friday, April 26, 2019 at 5:33:07 AM UTC-4, Daria Der wrote: I

7/9/19

7/9/19

Cistrome DB - Enquiry regarding batch download of bigwigs?

Dear Liu Lab Firstly I'd like to say thank you for Cistrome DB, its an amazing resource. I've

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Cistrome DB - Enquiry regarding batch download of bigwigs?

Dear Liu Lab Firstly I'd like to say thank you for Cistrome DB, its an amazing resource. I've

7/9/19

Abdo Abdo, Geri Law2

7/5/19

Nothing working with BETA-Cistrom

Hello Abdo, I'm another cistrome user. I too am experiencing similar failures with BETA on web

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Nothing working with BETA-Cistrom

Hello Abdo, I'm another cistrome user. I too am experiencing similar failures with BETA on web

7/5/19

WANG Zifeng, Jian Ma2

4/29/19

can't find the genome nib files after installing crispr-do locally

Hi, Before install crispr-do, you need to copy https://bitbucket.org/jianma/crisprdo/src/default/

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can't find the genome nib files after installing crispr-do locally

Hi, Before install crispr-do, you need to copy https://bitbucket.org/jianma/crisprdo/src/default/

4/29/19

agcresearc...@gmail.com, Ariane Lismer2

3/23/19

I am having the same problem so probably not a problem on your end... Ariane On Wednesday, March 20,

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I am having the same problem so probably not a problem on your end... Ariane On Wednesday, March 20,

3/23/19

Jian Ma, … Reza Fakhari5

10/29/18

Welcome to Cistrome Google Group! Here are some resources.

On Monday, June 20, 2011 at 11:49:46 PM UTC+4:30, Jian Ma wrote: Our Cistrome AP website: http://

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Welcome to Cistrome Google Group! Here are some resources.

On Monday, June 20, 2011 at 11:49:46 PM UTC+4:30, Jian Ma wrote: Our Cistrome AP website: http://

10/29/18

nicholas...@uconn.edu

10/23/18

Beta-basic Error Cistrome-Galaxy

I cannot seem to run BETA basic using a bed file from cistromeDB and my own DESeq2 expression data. I

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Beta-basic Error Cistrome-Galaxy

I cannot seem to run BETA basic using a bed file from cistromeDB and my own DESeq2 expression data. I

10/23/18

10/10/18

dm6 refgene file

Hello, I want to create a custom dm6 refgene file. I don't understand what wig file I should use

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dm6 refgene file

Hello, I want to create a custom dm6 refgene file. I don't understand what wig file I should use

10/10/18

10/10/18

SeqPos motif tool output help

Hi, Could someone point me to a resource that has an explaination for the output in the SeqPos motif

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SeqPos motif tool output help

Hi, Could someone point me to a resource that has an explaination for the output in the SeqPos motif

10/10/18

9/11/18

reset password link undeliverable

Hello, I am a novice user. I created an account a while back and have forgotten the password. Emails

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reset password link undeliverable

Hello, I am a novice user. I created an account a while back and have forgotten the password. Emails

9/11/18

8/17/18

Microarry using Galaxy

Hello every one. i would like to know if there is any way to use miroarry data in Galaxy\Cistrome.

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Microarry using Galaxy

Hello every one. i would like to know if there is any way to use miroarry data in Galaxy\Cistrome.

8/17/18

dc90...@gmail.com

6/22/18

Cannot to connect to cistrome ftp server

Hi, I'm trying to upload a large file (larger than 2G) to cistrome by ftp. But I cannot connect

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Cannot to connect to cistrome ftp server

Hi, I'm trying to upload a large file (larger than 2G) to cistrome by ftp. But I cannot connect

6/22/18

Abolfazl Doostparast, JurajSK2

4/6/18

Yes I was wondering the same thing??? The site is bit unclear about what are the actual target genes,

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Yes I was wondering the same thing??? The site is bit unclear about what are the actual target genes,

4/6/18

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