What are the bam files needed to use in ChipQC?

Question

[chansik]

Hi guys,

I'm trying to run ChipQC with my bam files and narrowPeak files.

But I have several different version of bam files with single dataset such as mapped bam, sorted bam, markduplicated bam

Which one should I use for chipQC?

Thank you in advance,

[chansik]

In the case of broad peak such as H3K4me1, as broad peakcall doesn't produce _peaks.narrowPeak format file, what file should I use?

If it is _peaks.broadPeak, then what are the appropriate parameter in peak caller instead of "narrow"?

Answer 1

[Friederike]

Which one should I use for chipQC?

You'll want to assess the BAM file that you used for peak calling. It's nicely summarized in the chart by the Harvard Bioinfo folks.

as broad peakcall doesn't produce _peaks.narrowPeak format file, what file should I use?

Any peak file that you are planning on using for your downstream analyses.

If you're dealing with a broad histone mark, some of the metrics will look different from the ones for sharp enrichments. It may be useful to read ChIPQC's original publication

[chansik]

Thank you, Friederike.

Yes, I was following what is summarized in the ChIP-seq Quality Assessment.

But as written in the website:

PeakCaller: Identifier string for peak caller used. Possible values include “raw”, “bed”, “narrow”, “macs”

and other website from bioconductor

It says,

So I'm confused because there is a "narrow" for narrowPeaks file but no parameter indicates for broadPeaks file.

Is it okay just run broadPeaks file with "narrow" parameter??

Again, thank you!

[Friederike]

The description you're showing is mostly concerned with parsing the file, i.e. identifying the correct format so that the tool knows where to extract the coordinates from. All the tool is doing (AFAIK) is to count the numbers of reads that overlap with the genomic intervals specified in the peaks file. If you used MACS, you can supply the xls file and use "macs" as a parameter, otherwise supplying a BED file (chr, start, end, p-value) should work, too.