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I am using ChIPQC to get quality metrics of my reads. I have .bam files and .narrowpeaks files. I created a sample csv file called sample1.csv. The sample.csv sheet can be found at this link.

https://docs.google.com/spreadsheets/d/12sovnIbEyH8CF8kRml7B6NLWt8z-Ck-iykBHvBe5Uqg/edit#gid=589685588

My code is the following:

samples <- read.csv('sample1.csv') View(samples) chipObj <- ChIPQC(samples, annotation="hg38")

However, I keep getting this error:

Error: Unable to process. Each bam file must be associated with at most one peakset.

Any help is appreciated

 QC ChIP • 1.0k views ADD COMMENT • link updated 3.5 years ago by Ram 44k • written 3.5 years ago by mropri ▴ 160 0 Entering edit mode

CSV is plain text content. Please paste the content here directly. Please do not ask us to visit some random Google Drive link.

See: How to Use Biostars Part-3: Formatting Text and Using GitHub Gists

Here is how your data would look, pasted directly after proper formatting:

SampleID Factor Replicate bamReads ControlID bamControl Peaks PeakCaller Tissue Condition 10A 1 H3K27ac 1 data/bams/10A_1_H3K_aligned.bam 10A_1_IgG data/bams/10A_1_IgG_aligned.bam data/peakcalls/10A_1_H3K_peaks_peaks.narrowPeak narrow NA NA 10A 2 H3K27ac 2 data/bams/10A_2_H3K_aligned.bam 10A_2_IgG data/bams/10A_2_IgG_aligned.bam data/peakcalls/10A_2_H3K_peaks_peaks.narrowPeak narrow NA NA CA1 1 H3K27ac 1 data/bams/CA1_1_H3K_aligned.bam CA_1_IgG data/bams/CA1_1_IgG_aligned.bam data/peakcalls/CA1_1_H3K_peaks_peaks.narrowPeak narrow NA NA CA1 3 H3K27ac 2 data/bams/CA1_3_H3K_aligned.bam CA1_3_IgG data/bams/CA1_3_IgG_aligned.bam data/peakcalls/CA1_3_H3K_peaks_peaks.narrowPeak narrow NA NA ADD REPLY • link 3.5 years ago by Ram 44k

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