I am trying to use ChIPQC on a set of bam files only (without peaks). I am using the version ChIPQC 1.8.3. So, I created a sample sheet with the bam file and no peak file. I am currently facing 2 issues in generating a ChIPQCreport.

1. I am unable to generate a html report for the experiment (error pasted below)

2. Individual bam file report works fine, but the total number of reads reported are almost double of what is being reported by samtools flagstats or FASTQC (please can you explain why this is happening? FASTQC reports total reads in the fastq file)

**Sample sheet **

SampleID Factor Replicate bamReads ControlID bamControl Peaks PeakCaller 1 Rep_1 GAF 1 R16C_3B-1_C2C12-GAGA_R1.bam Input R16C_3B-4_C2C12-In_R1.bam NA raw 2 Rep_2 GAF 2 R16C_3B-2_C2C12-GAGA_R1.bam Input R16C_3B-4_C2C12-In_R1.bam NA raw 3 Rep_3 GAF 3 R16C_3B-3_C2C12-GAGA_R1.bam Input R16C_3B-4_C2C12-In_R1.bam NA raw

**ChIPQC on the above sample sheet**

```
> try_qc = ChIPQC(try,annotation="mm10")
Rep_1 GAF 1 raw
Rep_2 GAF 2 raw
Rep_3 GAF 3 raw
Compiling annotation...
Computing metrics for 4 samples...
list
Bam file has 22 contigs
Calculating coverage histogram for chr10
Calculating SSD for chr10
Calculating shift for chr10
300 / 300
Counting reads in features for chr10
Calculating coverage histogram for chr11
Calculating SSD for chr11
Calculating shift for chr11
300 / 300
Counting reads in features for chr11
Calculating coverage histogram for chr12
Calculating SSD for chr12
Calculating shift for chr12
138 / 300list
Bam file has 22 contigs
Calculating coverage histogram for chr10
Calculating SSD for chr10
Calculating shift for chr10
300 / 300
Counting reads in features for chr10
Calculating coverage histogram for chr11
Calculating SSD for chr11
Calculating shift for chr11
300 / 300
Counting reads in features for chr11
Calculating coverage histogram for chr12
Calculating SSD for chr12
Calculating shift for chr12
138 / 300list
Bam file has 22 contigs
Calculating coverage histogram for chr10
Calculating SSD for chr10
Calculating shift for chr10
300 / 300
Counting reads in features for chr10
Calculating coverage histogram for chr11
Calculating SSD for chr11
Calculating shift for chr11
300 / 300
Counting reads in features for chr11
Calculating coverage histogram for chr12
Calculating SSD for chr12
Calculating shift for chr12
138 / 300list
Bam file has 22 contigs
Calculating coverage histogram for chr10
Calculating SSD for chr10
Calculating shift for chr10
300 / 300
Counting reads in features for chr10
Calculating coverage histogram for chr11
Calculating SSD for chr11
Calculating shift for chr11
300 / 300
Counting reads in features for chr11
Calculating coverage histogram for chr12
Calculating SSD for chr12
Calculating shift for chr12
138 / 300Warning message:
In ChIPQC(try, annotation = "mm10") :
No chromosomes specified in peaks, using all.
```

**ChIPQCreport **

```
> ChIPQCreport(try_qc)
Saving 10.1 x 7.46 in image
Saving 10.1 x 7.46 in image
Error in plotCorHeatmap(object, attributes = c(facetBy, colourBy)) :
No peaks to plot.
```

Thank you

Thanks Tom! I will try with the new version in that case :-)

If there are no peaks, we should still generate a report and simply skip the plots that only make sense if there are peaks, rather than report an error. We are already testing for this condition and reporting an error, we just need to change the test that prints out the "No peaks to plot" lines to something that returns cleanly.

I'll coordinate an appropriate response with Tom.

-Rory