Question: warning when using GenomicAlignments
0
gravatar for donny.dw
3 months ago by
donny.dw10
donny.dw10 wrote:

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]
genomicalignments rna-seq • 155 views
ADD COMMENTlink modified 5 weeks ago by ATpoint40k • written 3 months ago by donny.dw10
0
gravatar for ATpoint
5 weeks ago by
ATpoint40k
Germany
ATpoint40k wrote:

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.

ADD COMMENTlink written 5 weeks ago by ATpoint40k
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