Hi UCSC genome browser's technical group, I am Charlie and I recently used UCSC genome browser to try to visualize our ChIP sequencing data, and then I've encountered some problems. We used the ht-seq R package that developed by UC Riverside to do the analysis, and then output the analysis to a WIG file output. By carefully going through the WIG file format the UCSC genome browser supports, I think the output WIG file we have is supported by the browser. However, when I uploaded the this WIG file to custom track, it doesn't show out any peaks on the genome browser, even though the "score" is in the WIG file.
Interestingly, when I excerpt part of my WIG file (ex. I excerpt first 10,000 line), then the peaks display just fine. The following address is our WIG files: full file: http://radbio.lbl.gov:8080/ChIP/input_chr1.wig excerpt file: http://radbio.lbl.gov:8080/ChIP/input_chr1_part.wig Our WIG file is generated from the output of ht-seq package (in R) analysis, and the raw data is aligned by Bowtie with UCSC reference genome of hg18. Thanks for your help! -Charlie- _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
