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1–30 of 71
CLIP Tool Kit (CTK) is a software package for CLIP data analysis.
Documentation:
http://zhanglab.c2b2.columbia.
edu/index.php/CTK
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Zerui Wang
, …
Chaolin Zhang
3
6/26/24
Q&A
Input files as control
We do not use the input controls for our analysis using CTK. Chaolin On Jun 26, 2024, at 1:11 PM,
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Q&A
Input files as control
We do not use the input controls for our analysis using CTK. Chaolin On Jun 26, 2024, at 1:11 PM,
6/26/24
Baobao Geng
,
Chaolin Zhang
4
5/16/24
How to generate gene bed file
Thanks, I'll try it 在2024年5月15日星期三 UTC+8 18:54:31<Chaolin Zhang> 写道: Hi Baobao, We have not
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How to generate gene bed file
Thanks, I'll try it 在2024年5月15日星期三 UTC+8 18:54:31<Chaolin Zhang> 写道: Hi Baobao, We have not
5/16/24
chen chunxiao
2
3/4/24
Annotating and visualizing CLIP tags
I got it grom https://github.com/chaolinzhanglab/ctk Thanks! On Monday, March 4, 2024 at 3:29:48 PM
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Annotating and visualizing CLIP tags
I got it grom https://github.com/chaolinzhanglab/ctk Thanks! On Monday, March 4, 2024 at 3:29:48 PM
3/4/24
Wilfried Guiblet
1/24/24
Use of uninitialized value $refBase in pattern match (m//)
Hello CTK user group, I am having an issue running parseAlignment.pl on data mapped by STAR to a
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Use of uninitialized value $refBase in pattern match (m//)
Hello CTK user group, I am having an issue running parseAlignment.pl on data mapped by STAR to a
1/24/24
Luorongxin Yuan
1/4/24
CTK docker image?
Hello there, I'm wondering if there's a docker image for CTK? Many thanks, Mini
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CTK docker image?
Hello there, I'm wondering if there's a docker image for CTK? Many thanks, Mini
1/4/24
jianhong zhou
, …
Suvrajit Maji
3
11/13/23
Is conda ctk-cli package same as the CTK here?
Hi Jianhong, No, ctk-cli is a very different conda package: "Python interface for inspecting and
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Is conda ctk-cli package same as the CTK here?
Hi Jianhong, No, ctk-cli is a very different conda package: "Python interface for inspecting and
11/13/23
Erik Dassi
,
Chaolin Zhang
3
5/25/23
updating hg38 annotation
Dear Chaolin, many thanks for your reply. That is indeed a very useful suggestion! thanks a lot again
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updating hg38 annotation
Dear Chaolin, many thanks for your reply. That is indeed a very useful suggestion! thanks a lot again
5/25/23
Noura Tbeileh
5/24/23
License for CTK
Hello, I would like to use CTK for analysis but I am having trouble locating the license file in the
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License for CTK
Hello, I would like to use CTK for analysis but I am having trouble locating the license file in the
5/24/23
Cai Qi
,
Si Mi
2
1/31/23
mutation.random.0.bed failed: 6400
Hello Cai, I met the same problem. Did you solve it at last? Thanks, Si On Wednesday, December 9,
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mutation.random.0.bed failed: 6400
Hello Cai, I met the same problem. Did you solve it at last? Thanks, Si On Wednesday, December 9,
1/31/23
Xiao Lei
, …
Chaolin Zhang
8
12/7/21
Q&A
bed2annotation.pl fail
Hi Xuan, One thing you can check is the name of the chromosomes - they should be chrN instead of N,
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Q&A
bed2annotation.pl fail
Hi Xuan, One thing you can check is the name of the chromosomes - they should be chrN instead of N,
12/7/21
Andreas Pittroff
,
Chaolin Zhang
7
7/9/21
CITS.pl generates truncation sites > 1nt
I see, I guess I will try both - splitting and omitting - and compare the results. Thanks a lot for
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CITS.pl generates truncation sites > 1nt
I see, I guess I will try both - splitting and omitting - and compare the results. Thanks a lot for
7/9/21
coy...@gmail.com
,
Chaolin Zhang
3
5/25/21
Convert *.peak.sig.bed to narrowpeak format for IDR
Hi Chaolin, Thank you for the lightning fast reply! I'll give it a shot. Steve On Tuesday, May 25
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Convert *.peak.sig.bed to narrowpeak format for IDR
Hi Chaolin, Thank you for the lightning fast reply! I'll give it a shot. Steve On Tuesday, May 25
5/25/21
Zhang, Chaolin
12/21/20
Re: [EXTERNAL] About the analysis of PAR-CLIP data using CTK
Hi Yuwei, Hope you will find this helpful: https://zhanglab.c2b2.columbia.edu/index.php/
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Re: [EXTERNAL] About the analysis of PAR-CLIP data using CTK
Hi Yuwei, Hope you will find this helpful: https://zhanglab.c2b2.columbia.edu/index.php/
12/21/20
Cai Qi
12/6/20
call peak with significance without input files?
Hi CTK users: I am using CTK to analyze the eCLIP dataset. I have a question on the significance:
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call peak with significance without input files?
Hi CTK users: I am using CTK to analyze the eCLIP dataset. I have a question on the significance:
12/6/20
王程扬
11/28/20
what the fields stand for in output of CITS
Hi Professor Zhang, Sorry for one more question regarding the meaning which PH and PH0 stands for in
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what the fields stand for in output of CITS
Hi Professor Zhang, Sorry for one more question regarding the meaning which PH and PH0 stands for in
11/28/20
王程扬
,
Chaolin Zhang
3
11/28/20
Length of sequence and qualities differ
Hi Professor Zhang, Thank you very much for your prompt reply! Best, Chengyang On Sat, Nov 28, 2020
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Length of sequence and qualities differ
Hi Professor Zhang, Thank you very much for your prompt reply! Best, Chengyang On Sat, Nov 28, 2020
11/28/20
Cai Qi
,
Chaolin Zhang
3
11/26/20
Why eclip-seq only analyze the read2
Thanks, Dr. Zhang! On Thu, Nov 26, 2020 at 1:00 PM Chaolin Zhang <zhangc...@gmail.com> wrote
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Why eclip-seq only analyze the read2
Thanks, Dr. Zhang! On Thu, Nov 26, 2020 at 1:00 PM Chaolin Zhang <zhangc...@gmail.com> wrote
11/26/20
Cai Qi
10/5/20
Can't locate Common.pm at filtering step
I am in the process of using PAR-Clip protocol on the sample data. I use anaconda to install cutadapt
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Can't locate Common.pm at filtering step
I am in the process of using PAR-Clip protocol on the sample data. I use anaconda to install cutadapt
10/5/20
Cai Qi
9/30/20
Which protocol to use For HITS-clip
Hi Zhanglab: I am new to CLIP-SEQ. I want to follow the protocols of CTK-toolkit to go through the
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Which protocol to use For HITS-clip
Hi Zhanglab: I am new to CLIP-SEQ. I want to follow the protocols of CTK-toolkit to go through the
9/30/20
Chaolin Zhang
,
JIANG, CHONGMING
2
8/31/20
Re: [EXTERNAL] Three questions about the CTK-iCLIP pipeline usage. Thank Dr.Zhang so much!
Thank Dr.Zhang for your kindly response. I am new to the iCLIP-seq data analysis. For the paired end
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Re: [EXTERNAL] Three questions about the CTK-iCLIP pipeline usage. Thank Dr.Zhang so much!
Thank Dr.Zhang for your kindly response. I am new to the iCLIP-seq data analysis. For the paired end
8/31/20
gnili...@gmail.com
2
8/9/20
Q&A
error '-big failed: 9 at ~/ctk/CIMS.pl line 250` for CIMS.pl
After running seral times, I found everything is ok. So, it should be a problem about memory or
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Q&A
error '-big failed: 9 at ~/ctk/CIMS.pl line 250` for CIMS.pl
After running seral times, I found everything is ok. So, it should be a problem about memory or
8/9/20
maver...@gmail.com
7/13/20
Q&A
Kept getting "underfined symbol: PL_stack_sp_at /usr/lib64/perl5/Dynaloader.pm line 190" in running CIMS.pl
Hi there, I am new to CTK.. My issue is about lib path: I installed Math::CDF module locally and
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Q&A
Kept getting "underfined symbol: PL_stack_sp_at /usr/lib64/perl5/Dynaloader.pm line 190" in running CIMS.pl
Hi there, I am new to CTK.. My issue is about lib path: I installed Math::CDF module locally and
7/13/20
kotee...@gmail.com
, …
Cris
5
6/29/20
Q&A
CIMS.pl detected inconsistency... (2)
Hi, I figured it out. Everything was done correctly according to the suggestions. The problem was
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Q&A
CIMS.pl detected inconsistency... (2)
Hi, I figured it out. Everything was done correctly according to the suggestions. The problem was
6/29/20
Steve Coyne
,
Chaolin Zhang
4
5/13/20
Q&A
CITS calling discrepancy? Determining binding site at particular region (e.g. an exon with a large peak) at high resolution
One recommendation I have is that you can probably use RBFOX2 for a positive control to see if you
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Q&A
CITS calling discrepancy? Determining binding site at particular region (e.g. an exon with a large peak) at high resolution
One recommendation I have is that you can probably use RBFOX2 for a positive control to see if you
5/13/20
Cris Mar
,
coy...@gmail.com
2
5/6/20
Q&A
Motif enrichment software?
I have just set up and run meme-chip to run locally for my eCLIP analysis. I haven't tried HOMER.
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Q&A
Motif enrichment software?
I have just set up and run meme-chip to run locally for my eCLIP analysis. I haven't tried HOMER.
5/6/20
gnili...@gmail.com
,
Huijuan Feng
2
4/5/20
Q&A
where should I found the meaning of results' header
Hi, Thanks for choosing CTK. The count(>m, k) is the number of clustered mutation sites with k
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Q&A
where should I found the meaning of results' header
Hi, Thanks for choosing CTK. The count(>m, k) is the number of clustered mutation sites with k
4/5/20
yang chen
, …
Huijuan Feng
6
2/24/20
Q&A
tag2collapse.pl was killed
You're welcome. Pls let me know if you have any questions after rerun. Best, Huijuan On Monday,
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Q&A
tag2collapse.pl was killed
You're welcome. Pls let me know if you have any questions after rerun. Best, Huijuan On Monday,
2/24/20
yang chen
,
Huijuan Feng
6
2/24/20
Q&A
The unique tags number from parseAlignment.pl
Hi Huijuan, Thanks very much. It's my problem. I find the read number after using is
unread,
Q&A
The unique tags number from parseAlignment.pl
Hi Huijuan, Thanks very much. It's my problem. I find the read number after using is
2/24/20
yang chen
2/21/20
Q&A
What's the meaning of RNA in the rmsk.RNA.bed?
Hi Chaolin, When I remove the repetitive RNA, I find there are 6 kinds of RNA in the rmsk.RNA.bed
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Q&A
What's the meaning of RNA in the rmsk.RNA.bed?
Hi Chaolin, When I remove the repetitive RNA, I find there are 6 kinds of RNA in the rmsk.RNA.bed
2/21/20
wil.wsc...@gmail.com
,
Chaolin Zhang
2
2/5/20
Q&A
Support for C. elegans
Hi, You can actually do most of the analysis, except the step that annotates CLIP tags according to
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Q&A
Support for C. elegans
Hi, You can actually do most of the analysis, except the step that annotates CLIP tags according to
2/5/20