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 directly. -Ann On 1/12/11 10:50 AM, "Nick Schurch" <N.Schurch@dundee.ac.uk> 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?