Featurecount -- normalized Path error
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memoly101 • 0
@memoly101-19491
Last seen 2.4 years ago

Hi everybody,

I have just started using featuercounts and am new to this. Would you please help me with the folowing:

>fls <- dir("/path/to/bam/files/", "bam$")
> fls
 [1] "X_A.bam" 
> props <- propmapped(files=fls)
Error in normalizePath(files, mustWork = T) :
  path[1]="ENCFF064QSN.bam": No such file or directory

I can see that bam files are assigned but can't call them.

Thank you in advance, Memol

path Rsubread • 440 views
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Entering edit mode
@gordon-smyth
Last seen 1 hour ago
WEHI, Melbourne, Australia

You haven't told propmapped which directory the files are in so, naturally enough, it can't find them.

You need something like

bamdir <- "/path/to/bam/files"
bamfiles <- dir(bamdir, pattern = "bam$")
props <- propmapped( file.path(bamdir,bamfiles) )

Note that in the very latest version of Rsubread, you don't need to run propmapped at all, because the proportion of reads mapped is already returned as a data.frame from align() or subjunc().

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Thank you Gordon Smyth! I am going to try this. I really appreciate it!

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