Entering edit mode
José Luis Lavín
▴
280
@jose-luis-lavin-5529
Last seen 10.3 years ago
Hello everybody,
I've been told about a very nice R package called Repitools. It has
many
interesting features but the use of some of them remains a little
unclear
to me yet.
There are some subjects about this tool I'll have to ask about, in
this
list, but first of all I need to convert some BAM files into GRanges
objects.
To do so I read about BAM2GenomicRanges function. Reading the package
documentation, I tried to convert 3 BAM files into GRanges. I used the
following instructions:
*(where "/path/to/ANALYSIS/folder/" is the directory where my BAM
files are)
bgr <- BAM2GRanges('/path/to/ANALYSIS/folder/',
what = c("rname", "strand", "pos", "qwidth"),
flag = scanBamFlag(isUnmappedQuery = FALSE, isDuplicate = FALSE),
verbose = TRUE)
And I get this error message:
Reading BAM file AW-07.
[bam_header_read] bgzf_check_EOF: Invalid argument
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Error in open.BamFile(BamFile(file, index), "rb") :
SAM/BAM header missing or empty
file: '/path/to/ANALYSIS/folder/'
The BAM files I'm using here where produced by a tophat alignment and
used
in R previously for other analysis with this R code:
library(Rsamtools)
library(GenomicFeatures)
bamlist=list()
src_files=list.files(pattern="*.bam")
for(filename in src_files)
{
tmp=readBamGappedAlignments(filename)
bamlist[[length(bamlist)+1]]=GRanges(seqnames=rname(tmp),
ranges=IRanges(start=start(tmp),end=end(tmp)),
strand=rep("*",length(tmp)))
}
names(bamlist)=src_files
My question is, Why are now considered as invalid BAM files when they
previously worked as correct BAM files? Am I mistaken about the
meaning of
the error message?Did I miss something in the code?
Thanks in advance for your kind help.
JL
