Question

Importing/formatting .wig file with strand information

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3.7 years ago

k.smolyar • 0

I have a .wig file with three columns (Columns: Pos, Positive Strand, Negative Strand). I am trying to use import.wig into R, however I get the error "data length [1545] is not a sub-multiple or multiple of the number of rows [2]". When opening the wig in R, the columns are shifted and incorrectly filled. How can I import this strand information and maintain the integrity of the columns?

wig alignment R • 949 views

ADD COMMENT • link updated 3.7 years ago by Alex Reynolds 35k • written 3.7 years ago by k.smolyar • 0

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How was the wig file generated?

ADD REPLY • link 3.7 years ago by rpolicastro 13k

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The .wig file was generated using igvtools, exporting "counts" coverage information from a BAM file into the three columns.

ADD REPLY • link 3.7 years ago by k.smolyar • 0

score 0 · Answer 1 · 2020-08-13

Perhaps you could convert with BEDOPS wig2bed and import the resulting BED file into R via usual means:

$ wig2bed < in.wig > out.bed

If it is a correctly-formatted Wiggle file, then it should convert correctly. If it is not a correctly-formatted Wiggle file, then some awk swiss-knifing may be needed, as well as a bug report to IGV.