eCLIP peak calling

Question

[GiusiG]

Hi everyone,

I'm facing a problem calling peaks from a eCLIP experiment. I have 3 bam files: 2 replicates for one condition and a negative control. I don't know if this is the best option but I'm calling the peaks using MACS (from Galaxy), which is supposed to be for ChiP-seq and, for this reason, it doesn't give me the strand of the signal in the output file but I really need this information. Is there a way to tell MACS that I want the strand information to be kept? Or maybe is there a better way to call peaks for a CLIP experiment?

Once I have the bed files with the peaks I will use bedtools to extract the RNAs were I can find a peak for different factors.

Thank you in advance for your help

[Eric Lim]

We have had success with the CTK toolkits across various CLIP data. Installation can be a bit painful but I think it's worth the investment. https://zhanglab.c2b2.columbia.edu/index.php/CTK_Documentation

Answer 1

[sabrinakrakau]

Hi, we developed a tool called PureCLIP, which calls crosslink sites (or high resolution binding regions) from such data. It is available on GitHub https://github.com/skrakau/PureCLIP and can be installed via Bioconda. There is a branch on GitHub to integrate replicates, which will be released within the next month.

Answer 2

[Ashley]

Hi, I think Piranha is also a good strategy for analyzing CLIP-seq data. You can download from: http://smithlabresearch.org/software/piranha/ Thanks. Ashley