.BigWig file has more peaks than reads in .Bam file?
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Entering edit mode
18 months ago
Aryan ▴ 30

Hello,

I have two possibly related errors. The first one might be a result of the second one (which is what I am mainly asking about in this question).

  1. I am trying to use ChIPQC on R to get QC for my data. I have a bamfile named under variable bamfile of .bam extension, and bedfile is assigning the file name of a corresponding bigwig (.bw) file. I run,

    exp <- ChIPQCsample(bamfil,peaks = bedfil, annotation = "hg38",blacklist=BlackListFile, verbose = FALSE)

However, I get the following error:

Error in make.names(col.names, unique = TRUE) : 
  invalid multibyte string 1
In addition: Warning messages:
1: In read.table(file = file, header = header, sep = sep, quote = quote,  :
  line 1 appears to contain embedded nulls
2: In read.table(file = file, header = header, sep = sep, quote = quote,  :
  line 2 appears to contain embedded nulls
3: In read.table(file = file, header = header, sep = sep, quote = quote,  :
  line 3 appears to contain embedded nulls
4: In read.table(file = file, header = header, sep = sep, quote = quote,  :
  line 4 appears to contain embedded nulls
5: In read.table(file = file, header = header, sep = sep, quote = quote,  :
  line 5 appears to contain embedded nulls
  1. I am doubtful about the .bw file because it seems to have a lot more data entries than the BAM file has reads. For example, if I do,

    library(rtracklayer) library(GenomicAlignments)

    bam <- readGAlignments(bamfile) peaks <- import.bw(con = bedfile)

to access the data, and if I try to see the number of reads/peaks per chromosome, I get: enter image description here

Chromosome 1, for ex., has more peaks than reads?

chipseq chipqc bam bigwig R • 370 views
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