Function "fragmentCounts" is not working

[RileyMcMahon]

The function fragmentCounts is not working for my .bam files, I executed the following code from the Daim pipeline:

Extract restriction fragments

resFrag <- digestGenome(BSgenome.Mmusculus.UCSC.mm10)
resFrag
GRanges object with 6669641 ranges and 2 metadata columns:
seqnames ranges strand | digestBySize digestByProb
|
[1] chr1 1-3000192 * | 3000192 2.37e-05
[2] chr1 3000193-3000814 * | 622 3.54e-01
[3] chr1 3000815-3001049 * | 235 3.49e-01
[4] chr1 3001050-3001120 * | 71 4.23e-01
[5] chr1 3001121-3001796 * | 676 3.71e-01
... ... ... ... . ... ...
[6669637] chrY 90843572-90844088 * | 517 4.82e-01
[6669638] chrY 90844089-90844335 * | 247 3.68e-01
[6669639] chrY 90844336-90844497 * | 162 4.94e-01
[6669640] chrY 90844498-90844696 * | 199 3.77e-01
[6669641] chrY 90844697-91744698 * | 900002 1.11e-06

---

seqinfo: 21 sequences from mm10 genome

List sequence alignment data

bamPath <- c("Data/Sorted_Dam_1.bam", "Data/Sorted_Dam_2.bam", "Data/Sorted_Lhx1_1.bam", "Data/Sorted_Lhx1_2.bam")

Specify Dam and Dam-fusion samples

groupFactor <- factor(c(0, 0, 1, 1), levels = c(0, 1))

Count reads into restriction fragments

rawData <- fragmentCounts(bamPath, resFrag)

The function begins and does not show any errors, then it just stops without giving an output file. I am wondering what the issue might be.

[jma1991]

Thanks for posting this issue. You mentioned "then it just stops without giving an output file" - do you mean the variable is empty? The function doesn't produce any files on disk.

[RileyMcMahon]

Yes that is correct there is no "rawData" file on disk following the execution of:

rawData <- fragmentCounts(bamPath, resFrag)