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Question: Error reading BAM file with duplicated header in easyRNAseq and GenomicAlignments
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gravatar for Michael Dondrup
2.8 years ago by
Michael Dondrup • 10
Bergen, Norway
Michael Dondrup • 10 wrote:

I am trying to re-count a bunch of bam files that I have previously opened without problems in easyRNAseq and GenomicAlignments. But now I get. The bam files are seemingly valid and can be accessed by samtools, but the header contains few duplicated entries.

reads = readGAlignments('test.fastq.gz.clipped_M.bam.sorted.bam')

Error in GAlignments(seqnames = bamcols$rname, pos = bamcols$pos, cigar = bamcols$cigar,  :
  'seqlengths' must be an integer vector with unique names
In addition: Warning message:
In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste0(labels,  :
  duplicated levels in factors are deprecated

 

This is a related thread:

Error when reading bam file with duplicated header
easyrnaseq genomicalignments software error bam
ADD COMMENT • link •
modified 2.8 years ago by Martin Morgan ♦♦ 22k • written 2.8 years ago by Michael Dondrup • 10
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gravatar for Martin Morgan
2.8 years ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

Sorry for the delay, but I believe this is now fixed in GenomicAlignments / Rsamtools 1.4.2 / 1.20.5 (release) and 1.5.18 / 1.21.19 (devel).
ADD COMMENT • link written 2.8 years ago by Martin Morgan ♦♦ 22k

Thank you for fixing it. I can confirm that I can read and count the bam files again using GenomicAlignments and easyRNAseq, feels good :D

ADD REPLY • link written 2.8 years ago by Michael Dondrup • 10
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