Question: eCLIP peak calling
gravatar for GiusiG
4 months ago by
GiusiG0 wrote:

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

galaxy clip peak calling macs • 337 views
ADD COMMENTlink modified 11 weeks ago by Ashley50 • written 4 months ago by GiusiG0

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.

ADD REPLYlink written 4 months ago by Eric Lim1.3k
gravatar for sabrinakrakau
11 weeks ago by
sabrinakrakau0 wrote:

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

ADD COMMENTlink written 11 weeks ago by sabrinakrakau0
gravatar for Ashley
11 weeks ago by
Ashley50 wrote:

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

ADD COMMENTlink written 11 weeks ago by Ashley50
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