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chaolinzhanglab / ctk

CLIP Tool Kit (CTK)
http://zhanglab.c2b2.columbia.edu/index.php/CTK
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Pair-End Data Processing with CTK? #6

Open luckyvivi opened 6 months ago

luckyvivi commented 6 months ago

Hi Zhang Lab team,

Firstly, I'd like to commend you on the excellent single-end CLIP data analysis tutorial available on your site; it's been incredibly useful. https://zhanglab.c2b2.columbia.edu/index.php/ICLIP_data_analysis_using_CTK https://zhanglab.c2b2.columbia.edu/index.php/PARCLIP_data_analysis_using_CTK

I'm currently working with pair-end CLIP data and was wondering if you have any recommendations or resources on adapting the CTK workflow for pair-end data processing?

Any guidance or pointers you could provide would be greatly appreciated.

zhangchaolin commented 6 months ago

Hi, Xiaowen,

Since CLIP tags are in generally short, we typically do not think paired-end reads are necessary.

Chaolin

On Mar 14, 2024, at 2:18 AM, Xiaowen @.***> wrote:

Hi Zhang Lab team,

Firstly, I'd like to commend you on the excellent single-end CLIP data analysis tutorial available on your site; it's been incredibly useful. https://zhanglab.c2b2.columbia.edu/index.php/ICLIP_data_analysis_using_CTK https://zhanglab.c2b2.columbia.edu/index.php/PARCLIP_data_analysis_using_CTK

I'm currently working with pair-end CLIP data and was wondering if you have any recommendations or resources on adapting the CTK workflow for pair-end data processing?

Any guidance or pointers you could provide would be greatly appreciated.

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luckyvivi commented 6 months ago

Hi, Chaolin,

Thanks for the clarification. I understand that CLIP data is predominantly single-end, however, in my recent analyses of public datasets, I've noticed some newer data are provided as pair-end, for example, this link: https://www.ncbi.nlm.nih.gov/sra?term=SRX17144017. Should I merge R1 and R2 at the start and analyze them as single-end, or is there another approach you recommend?

By the way, I have another question regarding PAR-CLIP data, is a low alignment ratio (around 5%) normal, or maybe due to not trimming all barcodes?

Xiaowen