warning when using GenomicAlignments

Question

[donny.dw]

I have 50 warning when using summarizeOverlaps to caculate read count. Here is the code.

sampleTable <- read.csv("./sampleTable.csv", row.names = 1)
library("Rsamtools")
filenames <- file.path("../BAM", sampleTable$SampleName)
bamfiles <- BamFileList(filenames, yieldSize=2000000)
bamfiles
seqinfo(bamfiles[1])
library("GenomicFeatures")
gtffile <- file.path("./UCSC_hg38.gtf")
txdb <- makeTxDbFromGFF(gtffile, format = "gtf", circ_seqs = character())
txdb
ebg <- exonsBy(txdb, by="gene")
ebg
library("GenomicAlignments")
library("BiocParallel")
multicoreParam <- MulticoreParam(workers = 32)
register(multicoreParam)
se<-summarizeOverlaps(features=ebg, reads=bamfiles,mode="Union",singleEnd=FALSE,
                      ignore.strand=TRUE,fragments=TRUE,BPPARAM=multicoreParam)

But I do get read counts of 26483 gene. Can I some suggestions how to avoid this? Should I ignore it?

Warning message:

50: In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270759v1_alt, chr1_KI270761v1_alt, chr1_KI270762v1_alt, chr1_KI270763v1_alt, chr1_KI27076
5v1_alt, chr1_KI270766v1_alt, chr1_KI270892v1_alt, chr2_GL383521v1_alt, chr2_GL383522v1_alt, chr2_GL582966v2_alt, chr2_KI270767v1_alt, chr2_KI270768v1_alt, chr2_KI270769v1
_alt, chr2_KI270770v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270776v1_alt, chr2_KI270893v1_alt, chr3_GL383526v1_alt, chr3_JH636055v2_alt, chr3_KI270777v1_al
t, chr3_KI270779v1_alt, chr3_KI270780v1_alt, chr3_KI270782v1_alt, chr3_KI270783v1_alt, chr3_KI270784v1_alt, chr3_KI270895v1_alt, chr3_KI270924v1_alt, chr3_KI270934v1_alt, 
chr3_KI270935v1_alt, chr3_KI270936v1_alt, chr3_KI270937v1_alt, chr4_GL000257v2_alt, chr4_GL383527v1_alt, chr4_KI270789v1_alt, chr4_KI270896v1_alt, chr4_KI270925v1_alt, chr
5_GL339449v2_alt, chr5_GL949742v1_alt, chr5_KI270791v1_alt, chr5_KI270792v1_ [... truncated]

Answer 1

[ATpoint]

It is a warning, not an error. It is saying that there are chromosome (seqnames) in one or the other GRanges that is not in the respective other one. You can probably ignore it.