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Importing local bigwig fails on some files in windows #128

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LinearParadox opened this issue Jul 31, 2024 · 0 comments
Open

Importing local bigwig fails on some files in windows #128

LinearParadox opened this issue Jul 31, 2024 · 0 comments

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@LinearParadox
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Hi all,

Importing a bigwig locally is seemingly failing on windows with the error:

x<-rtracklayer::import('Normal_Tissue_merged.norm.bw', format="bigwig")
Error in seqinfo(ranges) : UCSC library operation failed
In addition: Warning message:
In seqinfo(ranges) :
  Couldn't openNormal_Tissue_merged.norm.bw

Oddly enough, this seems to work with bigwig files from individual samples. However, when I try to open a merged file I get this error. As far as I can tell, the file was created using:

# first set of tech reps
~/software/WiggleTools/bin/wiggletools mean \
../data/tracks_v2/Tumor_Tissue_1.norm.bw \
../data/tracks_v2/Tumor_Tissue_2.norm.bw \
> tmp.wig

/data/devtools/ucsc_tools/bedGraphToBigWig \
tmp.wig \
~/refs/human_GRCh37/hg19.sizes \
../data/tracks_v2/Tumor_Tissue_merge_A.norm.bw

# second set of tech reps
~/software/WiggleTools/bin/wiggletools mean \
../data/tracks_v2/Tumor_Tissue_3.norm.bw \
../data/tracks_v2/Tumor_Tissue_4.norm.bw \
../data/tracks_v2/Tumor_Tissue_5.norm.bw \
> tmp.wig

/data/devtools/ucsc_tools/bedGraphToBigWig \
tmp.wig \
~/refs/human_GRCh37/hg19.sizes \
../data/tracks_v2/Tumor_Tissue_merge_B.norm.bw

the wig files like "Tumor_Tissue_1.norm.bw" seem to work, but files like tumor_tissue_merge do not.

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