Pair-End Data Processing with CTK?

[luckyvivi]

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]

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

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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. — Reply to this email directly, view it on GitHub <#6>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEJPO7PV363BRX4TWNQCMO3YYE6JZAVCNFSM6AAAAABEVO4DJWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGE4DKNJRHAZTENI>. You are receiving this because you are subscribed to this thread.

[luckyvivi]

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