CTK User Group

We do not use the input controls for our analysis using CTK. Chaolin On Jun 26, 2024, at 1:11 PM,

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

I got it grom https://github.com/chaolinzhanglab/ctk Thanks! On Monday, March 4, 2024 at 3:29:48 PM

Hello CTK user group, I am having an issue running parseAlignment.pl on data mapped by STAR to a

Hello there, I'm wondering if there's a docker image for CTK? Many thanks, Mini

Hi Jianhong, No, ctk-cli is a very different conda package: "Python interface for inspecting and

Dear Chaolin, many thanks for your reply. That is indeed a very useful suggestion! thanks a lot again

Hello, I would like to use CTK for analysis but I am having trouble locating the license file in the

Hello Cai, I met the same problem. Did you solve it at last? Thanks, Si On Wednesday, December 9,

Hi Xuan, One thing you can check is the name of the chromosomes - they should be chrN instead of N,

I see, I guess I will try both - splitting and omitting - and compare the results. Thanks a lot for

Hi Chaolin, Thank you for the lightning fast reply! I'll give it a shot. Steve On Tuesday, May 25

Hi Yuwei, Hope you will find this helpful: https://zhanglab.c2b2.columbia.edu/index.php/

Hi CTK users: I am using CTK to analyze the eCLIP dataset. I have a question on the significance:

Hi Professor Zhang, Sorry for one more question regarding the meaning which PH and PH0 stands for in

Hi Professor Zhang, Thank you very much for your prompt reply! Best, Chengyang On Sat, Nov 28, 2020

Thanks, Dr. Zhang! On Thu, Nov 26, 2020 at 1:00 PM Chaolin Zhang <zhangc...@gmail.com> wrote

I am in the process of using PAR-Clip protocol on the sample data. I use anaconda to install cutadapt

Hi Zhanglab: I am new to CLIP-SEQ. I want to follow the protocols of CTK-toolkit to go through the

Thank Dr.Zhang for your kindly response. I am new to the iCLIP-seq data analysis. For the paired end

After running seral times, I found everything is ok. So, it should be a problem about memory or

Hi there, I am new to CTK.. My issue is about lib path: I installed Math::CDF module locally and

Hi, I figured it out. Everything was done correctly according to the suggestions. The problem was

One recommendation I have is that you can probably use RBFOX2 for a positive control to see if you

I have just set up and run meme-chip to run locally for my eCLIP analysis. I haven't tried HOMER.

Hi, Thanks for choosing CTK. The count(>m, k) is the number of clustered mutation sites with k

You're welcome. Pls let me know if you have any questions after rerun. Best, Huijuan On Monday,

Hi Huijuan, Thanks very much. It's my problem. I find the read number after using is

Hi Chaolin, When I remove the repetitive RNA, I find there are 6 kinds of RNA in the rmsk.RNA.bed

Hi, You can actually do most of the analysis, except the step that annotates CLIP tags according to