CRISPRAnalyzeR

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Dear CRISPRAnalyzeR users,

welcome to the google group help forum for caRpools and CRSIRPAnalyzeR.

CRISPRAnalyzeR is a web-based application to analyse, annotate and document pooled CRISPR screens in a single workflow.

CRISPRAnalyzeR is available from http://www.crispr-analyzer.org or via the GitHub page at http://www.github.com/boutroslab/CRISPRAnalyzeR .

It can be installed locally using a pre-configured docker container which you can also find on the webpage.

A PrePrint is available at http://biorxiv.org/content/early/2017/02/20/109967 .

Since CRISPRAnalyzeR is still in development, I am looking forward to all kinds of feedback.

Please post any questions, suggestions and problems here.

You can also find me on twitter @winterj86 .

Best,

Jan

0 selected

Jan Winter, Vineet Dalal4

4/8/20

CRISPRAnalyzeR now available for a local installation!

Hey Jan, I hope you are doing well. I have been trying for a couple of days to analyse my data using

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CRISPRAnalyzeR now available for a local installation!

Hey Jan, I hope you are doing well. I have been trying for a couple of days to analyse my data using

4/8/20

Jan Winter

2/24/17

Announcement

Changelog / Updates

CRISPRAnalyzeR V1.17 has been released! V 1.17 (latest) - fixed BAGEL issues - added the possibility

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Announcement

Changelog / Updates

CRISPRAnalyzeR V1.17 has been released! V 1.17 (latest) - fixed BAGEL issues - added the possibility

2/24/17

Elen Louwagie, hailey2

4/2/22

Disconnected from the server

I have the same issue !! I uploaded txt files, but still have a connection problem. 2021년 7월 7일 수요일

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Disconnected from the server

I have the same issue !! I uploaded txt files, but still have a connection problem. 2021년 7월 7일 수요일

4/2/22

Devin Dersh

4/26/21

File upload not working?

Hello, I'm trying to upload fastq.gz files in the data upload section, but receive an error just

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File upload not working?

Hello, I'm trying to upload fastq.gz files in the data upload section, but receive an error just

4/26/21

Maria Miquel, … Florian Heigwer6

10/29/20

Online version

in addition I tested the version available via docker run -p 8000:8000 boutroslab/crispranalyzer:

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Online version

in addition I tested the version available via docker run -p 8000:8000 boutroslab/crispranalyzer:

10/29/20

Ruth Hanna, Florian Heigwer2

10/29/20

site down

Dear all, I am Florian, a Senior Scientist in Michael Boutros Group. I am now working (when I find

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site down

Dear all, I am Florian, a Senior Scientist in Michael Boutros Group. I am now working (when I find

10/29/20

john alexander, … Florian Heigwer3

10/29/20

disconnected from the server

Dear all, I am Florian, a Senior Scientist in Michael Boutros Group. I am now working (when I find

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disconnected from the server

Dear all, I am Florian, a Senior Scientist in Michael Boutros Group. I am now working (when I find

10/29/20

Mithun Das, … Florian Heigwer4

10/29/20

Q&A

Unfortunately, the ENSEMBL biomaRt web-service seems to be offline.

Often the biomart service disconnects if there are to many requests from one site. After a while this

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Q&A

Unfortunately, the ENSEMBL biomaRt web-service seems to be offline.

Often the biomart service disconnects if there are to many requests from one site. After a while this

10/29/20

stayfun elang

9/11/20

disconnected from server

Facing the same issues as other users, the online version turns grey and the version post uploading

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disconnected from server

Facing the same issues as other users, the online version turns grey and the version post uploading

9/11/20

Lin Tian

7/18/20

the ENSEMBL biomaRt web-service seems to be offline

Hi everyone, When I ran the crispr-analyzer using the demo data, the analysis was stopped because of

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the ENSEMBL biomaRt web-service seems to be offline

Hi everyone, When I ran the crispr-analyzer using the demo data, the analysis was stopped because of

7/18/20

Vineet Dalal

4/7/20

sgRNA Re-Evaluation stalled at 50%

Hey, I performed a CRISPR KO screen and used the CRISPRAnalyzer platform. My analysis is being done

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sgRNA Re-Evaluation stalled at 50%

Hey, I performed a CRISPR KO screen and used the CRISPRAnalyzer platform. My analysis is being done

4/7/20

Aliaksandra Radzisheuskaya

3/8/20

No alignment using data.extract

Hello, I have a sgRNA pattern CACC+G+20 nucleotides+GTT. When I am running this data.extract line, I

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No alignment using data.extract

Hello, I have a sgRNA pattern CACC+G+20 nucleotides+GTT. When I am running this data.extract line, I

3/8/20

Mithun Das

2/9/20

DESeq2 Hit calculation could not be performed_Error message

Hi all I am getting an error message saying "DESeq2 Hit calculation could not be performed"

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DESeq2 Hit calculation could not be performed_Error message

Hi all I am getting an error message saying "DESeq2 Hit calculation could not be performed"

2/9/20

David Schöndorf, john alexander2

1/13/20

Upload of Data

I've got the same problem too. I installed it via docker and got the same error too On Thursday,

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Upload of Data

I've got the same problem too. I installed it via docker and got the same error too On Thursday,

1/13/20

Wanlu Du

7/23/19

Upload issue

Hello! I can't upload my data via the upload screen tab (it shows red bar after the upload runs

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Upload issue

Hello! I can't upload my data via the upload screen tab (it shows red bar after the upload runs

7/23/19

Marlene Vreni Arroyo

7/23/19

Upload issue

Hello, I am unable to upload my data files. The file begins to upload and runs fine up until the end

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Upload issue

Hello, I am unable to upload my data files. The file begins to upload and runs fine up until the end

7/23/19

Julien Dessapt

2/20/19

Analysis stalled at 9%

Hi, I've been trying to use CRISPRanalyzer to look at some datas of mine but I've ran into

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Analysis stalled at 9%

Hi, I've been trying to use CRISPRanalyzer to look at some datas of mine but I've ran into

2/20/19

csuc...@gmail.com

9/14/18

EdgeR Analysis Failed

I am trying to run CRISPR-AnalyzeR but the analysis keeps failing at the EdgeR analysis. I keep

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EdgeR Analysis Failed

I am trying to run CRISPR-AnalyzeR but the analysis keeps failing at the EdgeR analysis. I keep

9/14/18

Jared Wollman

7/31/18

Q&A

no technical replicate

Hi, We are trying to analyze a single independent experiment with four different groups. We are able

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Q&A

no technical replicate

Hi, We are trying to analyze a single independent experiment with four different groups. We are able

7/31/18

Rafael Blasco, Jan Winter2

5/15/18

Program stalled at 91%

Hi Rafael, please untick the FASTQ Quality report available in the data upload settings. When my PhD

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Program stalled at 91%

Hi Rafael, please untick the FASTQ Quality report available in the data upload settings. When my PhD

5/15/18

mat...@gmail.com

4/11/18

Q&A

Analysis without replicates

Hi Jan, I have a question. Is it possible to do the analysis without replicates? My problem is that I

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Q&A

Analysis without replicates

Hi Jan, I have a question. Is it possible to do the analysis without replicates? My problem is that I

4/11/18

Yunyu

3/15/18

Q&A

Reverse complementary sequences in FASTQ data

Hi, I am trying to analyze our fastq.gz data along with the GeckoV2 A+B library which provided online

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Q&A

Reverse complementary sequences in FASTQ data

Hi, I am trying to analyze our fastq.gz data along with the GeckoV2 A+B library which provided online

3/15/18

Klaas de Lint, … Jan Winter10

3/14/18

"Something went wrong during Hit Calling calculations."

Amazing! Thanks in advance :) Am Montag, 12. März 2018 14:43:43 UTC+1 schrieb Agata Szymanek: Hi Jan!

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"Something went wrong during Hit Calling calculations."

Amazing! Thanks in advance :) Am Montag, 12. März 2018 14:43:43 UTC+1 schrieb Agata Szymanek: Hi Jan!

3/14/18

Shengb Suo, Jan Winter2

3/8/18

ERROR: An error has occurred. Check your logs or contact the app author for clarification.

hi Shengbao, sorry to hear that the undelrying shiny-server is crashing. This happens in the case

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ERROR: An error has occurred. Check your logs or contact the app author for clarification.

hi Shengbao, sorry to hear that the undelrying shiny-server is crashing. This happens in the case

3/8/18

stephen mclaughlin, Jan Winter3

2/27/18

Docker trouble

Thank you Jan! This fixes my problem. Best, Stephen On Tuesday, February 27, 2018 at 5:42:55 PM UTC-5

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Docker trouble

Thank you Jan! This fixes my problem. Best, Stephen On Tuesday, February 27, 2018 at 5:42:55 PM UTC-5

2/27/18

Shengb Suo, Jan Winter2

1/11/18

Q&A

DESeq2 Hit calculation could not be performed.

Hi Shengbao, sorry for having overseen your post! Please only upload raw data or read count files

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Q&A

DESeq2 Hit calculation could not be performed.

Hi Shengbao, sorry for having overseen your post! Please only upload raw data or read count files

1/11/18

Yulin, Jan Winter2

5/24/17

Is it possible to download all the analysis results in sgRNA level?

HI Yulin, thanks for your question. Right now you cannot download the underlying raw data directly.

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Is it possible to download all the analysis results in sgRNA level?

HI Yulin, thanks for your question. Right now you cannot download the underlying raw data directly.

5/24/17

Kartik Chandran, Jan Winter2

5/17/17

CRISPRAnalyzeR run stalling at 91%

Hi Kartik, sorry for my late response. We had some issues with the Gecko library before that should

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CRISPRAnalyzeR run stalling at 91%

Hi Kartik, sorry for my late response. We had some issues with the Gecko library before that should

5/17/17

Johannes Schlondorff, Jan Winter3

5/1/17

No alignment with Brunello library file

Dear Jan, Thanks for looking into this. I think I may have figured out the issue. I repeated the

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No alignment with Brunello library file

Dear Jan, Thanks for looking into this. I think I may have figured out the issue. I repeated the

5/1/17

Jan Winter

4/1/17

Please update to 1.141 (latest) from today since the Ensembl Database introduced changes!

Dear all, please make sure to update to the latest version as the Ensembl database received some

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Please update to 1.141 (latest) from today since the Ensembl Database introduced changes!

Dear all, please make sure to update to the latest version as the Ensembl database received some

4/1/17

Jan Winter

12/6/16

CRISPRAnalyzeR Release candidate out soon

Dear all, I know you still experience a lot of issues with disconnects - which unfortunately are

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CRISPRAnalyzeR Release candidate out soon

Dear all, I know you still experience a lot of issues with disconnects - which unfortunately are

12/6/16

Anuja Sathe, Jan Winter3

11/1/16

Q&A

RefSeq ID in library file/mapped reads

Hi Jan, Sorry I meant RefSeq NM for mRNA. Thanks a lot! On Tuesday, November 1, 2016 at 1:33:57 PM

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Q&A

RefSeq ID in library file/mapped reads

Hi Jan, Sorry I meant RefSeq NM for mRNA. Thanks a lot! On Tuesday, November 1, 2016 at 1:33:57 PM

11/1/16