I am a PSU student at the College of Medicine. I have minimal bioinformatics and computer programing background. I was introduced to galaxy during televisied genomics course. I believe I am using galaxy on the cloud.
I am trying to display ChIP-CHIP data on UCSC. I have downloaded the gff file (attached; NCBI/GEO # GSM413116) and uploaded it into galaxy (using get data; upload file). The initial publication converted gff file to wig file for upload into UCSC. I could not find this function in Galaxy so I tried converting to bed file instead (convert formats; gff-to-bed). When I do this and upload into UCSC I do not get the peak hight (score difference) at each site (column 6 of gff file; score--which appears to convert to all 0s in bed file), only the locations are annotated but not the score. Is there something I am doing wrong in the conversion to a bed file or alternatively is there a way to convert the intial gff file into a wig file? Any help would be greatly appreciated!
Thanks,
Lindsay Horvath