warning when using GenomicAlignments
1
0
Entering edit mode
9 months ago
donny.dw ▴ 10

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]
RNA-Seq GenomicAlignments • 263 views
ADD COMMENT
0
Entering edit mode
6 months ago
ATpoint 47k

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 COMMENT

Login before adding your answer.

Traffic: 3118 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6