How to analyse clip-seq data?

05 May 2016 1 2K Report

I recently find a Clip-seq data of an RNA binding Protein from Encode database, The files includes both raw (fastq) and processed data (bam, bigBed narrowPeak). How can I analyse these data to find the target binding RNA?

Ashwani Jha

HI,

You can use samtools to convert bam to sam (text format). The bam contains the location of mapped reads (Chromosme, Start and End cordinates). I think the files in ENCODE contains the name of RBP/TF name in the extension. You may want to read this page also https://genome.ucsc.edu/ENCODE/fileFormats.html.

P.S. Be careful about the assembly.

Regards

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