Remove the intron peaks from the genome browser

Question

[bright602]

Hi, I finish my mapping and upload the bigwig files to IGV. However, I found lots of intron regions also have peaks, could someone tell me how to remove those intron peaks?

Thanks for your help!

[seidel]

What kind of data is this? How did you generate your tracks? If it's RNA Seq data, and you used bedtools to generate coverage, you might try the -split option. There's a million ways to generate coverage tracks - guessing what you did, or why you want to hide introns without knowing what kind of data it is, is sort of useless. Please tell us what you have, what you did, how you did it, and why you did it.

[bright602]

Thanks for your reply. Yes, they are RNAseq data and I tried using the following two commands to get the bigwig files. But I don't know why there are intron peaks on those RNAseq tracks.

bedtools genomecov -ibam ${file}.unique.bam -bg | sort -k1,1 -k2,2n > ${file}.bg

${script}/bedGraphToBigWig ${file}.bg ${script}/${genome}.chrom.sizes ${file}.bw

Answer 1

[seidel]

Given that this is RNA Seq data, when you create your coverage track using bedtools, supply the -split option, which will account for the space between exons and not add coverage to display. The figure shows the difference with and without split. Modifying your own code:

bedtools genomecov -ibam input.bam -bg -split | sort -k1,1 -k2,2n > output.bg