My apologies. I mis-spoke. (Mis-typed?)

The wiggles program is in the TopHat distribution:

$ ls
AUTHORS            fix_map_ordering    sam_juncs
COPYING            gtf_juncs        segment_juncs
README            juncs_db        sra_to_solid
bed_to_juncs        library_stats        tophat
closure_juncs        long_spanning_reads    tophat_reports
contig_to_chr_coords    mask_sam        wiggles
extract_reads        prep_reads

Very sorry for the mixup.

I am cc-ing Adam Baxter, who modified wiggles to run like so:

samtools view accepted_hits.bam | wiggles > coverage.wig

If you would like a copy of his modified version, feel free to contact him


On 1/12/11 10:50 AM, "Nick Schurch" <> wrote:

> HI,
> I can't find any mention of a program called 'wiggles' in the source
> code distribution of bowtie 0.12.7, or out install of 0.12.3. Could
> someone point me to the location of the program in the bowtie file
> structure, or failing that a website for it?

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