Question: featureCounts Does Not Correctly Parse File Names
0
gravatar for wunderl
10 days ago by
wunderl0
wunderl0 wrote:

When using Rsubread v 1.28.1 it sucessfully parsed my input file names by removing the file path and just keeping the names. As of the current version, however, the names contain the entire file path, this makes for very long and ugly column names.

Example

Setup

files: /path/to/file/here/file1.bam; /path/to/file/here/file2.bam countData=featureCounts(.....)


1.28.1

colnames(countData$counts) [1] file1.bam
[2] file2.bam


1.34.0

colnames(countData$counts) [1] X.path.to.file.here.file1.bam [2] X.path.to.file.here.file2.bam

rsubread featurecounts • 44 views
ADD COMMENTlink modified 9 days ago by Gordon Smyth37k • written 10 days ago by wunderl0
Answer: featureCounts Does Not Correctly Parse File Names
1
gravatar for Gordon Smyth
9 days ago by
Gordon Smyth37k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth37k wrote:

I guess the reason for the change was probably because file names without paths might not be unique. For example, we might have

files <- c("path1/file1.bam", "path2/file1.bam")

so that removing the paths would result in duplicate column names.

If you don't like it you can easily change the column names yourself by

colnames(countData$counts) <- basename(colnames(countData$counts))
ADD COMMENTlink modified 9 days ago • written 9 days ago by Gordon Smyth37k
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