I get the above message while attempting to convert into bigwig format the dm3
phastcons scores (as downloaded from
ftp://hgdownload.cse.ucsc.edu/goldenPath/dm3/phastCons15way)
The error occurs only with chromosomes chr2R, X, 3L, and 3R
gunzip -c chr2R.pp.gz | wigToBigWig -clip stdin dm3_chromeSizes.tab
dm3_chr2R_phastCons15way.bw
There's more than one value for chr2R base 5000001 (in coordinates that start
with 1).
gunzip -c chr3R.pp.gz | wigToBigWig -clip stdin dm3_chromeSizes.tab
dm3_chr3R_phastCons15way.bw
There's more than one value for chr3R base 7000001 (in coordinates that start
with 1).
gunzip -c /chrX.pp.gz | wigToBigWig -clip stdin dm3_chromeSizes.tab
dm3_chrX_phastCons15way.bw
There's more than one value for chrX base 12000001 (in coordinates that start
with 1).
gunzip -c chr3L.pp.gz | wigToBigWig -clip stdin dm3_chromeSizes.tab
dm3_chr3L_phastCons15way.bw
There's more than one value for chr3L base 7000001 (in coordinates that start
with 1).
I'd appreciate understanding if
I am mis-using the tools
there are some errors in upstream processes generating the phastCons
wig files
there are some issues with wigToBigWig
other ???
My purpose in this converstion is to provide fast random access to the
phastCons scores via subsequent calls to bigWigToWig for a analysis I am
developing.
If there are other (better) ways of acheiving this, I would be similarly
obliged to learn.
Thanks,
Malcolm Cook
Stowers Institute for Medical Research - Bioinformatics
Kansas City, Missouri USA
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