summarizeOverlaps warning A. thaliana differential expression

Question

[eva.lucarelli]

Hello, I am currently working on a differential expression tutorial regarding gene expression in Arabidopsis thaliana.

At some point in the exercise, we use the function summarizeOverlaps, and I get the following warning. Does anyone know what it means and how to solve the problem? Here is the code we use until then:

data_folder <- "~/Desktop/BIN201_Exercise_5_DEseq-2/data/"
bamfiles <- BamFileList(dir(path = data_folder, pattern="sorted.bam", full.names = TRUE))
txdb = makeTxDbFromGFF(paste0(data_folder, "Arabidopsis.gtf"), format="gtf")
ebg = exonsBy(txdb, by="gene")
se = summarizeOverlaps(features=ebg, reads=bamfiles, mode="Union", singleEnd=TRUE, ignore.strand=TRUE )

Warning messages:

1: In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': ChrC, ChrM
  - in 'y': chloroplast, mitochondria
  Make sure to always combine/compare objects based on the same reference
  genome (use suppressWarnings() to suppress this warning).

2: In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': ChrC, ChrM
  - in 'y': chloroplast, mitochondria
  Make sure to always combine/compare objects based on the same reference
  genome (use suppressWarnings() to suppress this warning).

3: In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': ChrC, ChrM
  - in 'y': chloroplast, mitochondria
  Make sure to always combine/compare objects based on the same reference
  genome (use suppressWarnings() to suppress this warning).

4: In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': ChrC, ChrM
  - in 'y': chloroplast, mitochondria
  Make sure to always combine/compare objects based on the same reference
  genome (use suppressWarnings() to suppress this warning).

Thank you in advance for the answers!

Cheers,

Eva