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ChIP QC

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
• 1,431 views • link
updated by Ram Ram • written by mropri mropri

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
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written by Ram Ram

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