Problem in calling peak by MACS3

Question

[daffodil]

Hi everyone, I have the CUT&RUN data in my sample. I have generated bigwig file by deepTools When I compare my bigwig files and bed files (after MACS3 peak calling), I see that there are many peaks which are appearing when I visualize the bigwig files but not in bed files. Which other parameters I can play with in MACS to get all the peaks. Best regards Masomeh

[Pierre Lindenbaum]

• Error during demultiplexing by bcl2fastq
• RNA_seq
• Normalization of Bigwig file
• Bowtie alignment
• Adapter Removing
• BigWig file in IGV
• Bar plot in R
• fastq Groomer action
• meaning of the Per tile sequence quality

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[ATpoint]

You really need to add some plots or images to illustrate. Right now it's "my cake looks different than on the bakery website" without any details what you did.