Hi Brad & Lance, I've been using Brad's bam_to_bigwig tool in Galaxy but realized today (with a new dataset using a splice-aware mapper) that it doesn't seem to be ignoring CIGAR N operators where a read is split over an intron. Looking over Brad's Python script which calculates the coverage to write an intermediate wiggle file, this is done with the samtools via pysam. It is not obvious to me if this can be easily modified to ignore introns. Is this possible Brad?
I wasn't aware of Lance's rival bam_to_bigwig tool in the ToolShed till now, and that does talk about this issue. It has a boolean option to ignore gaps when computing coverage, recommended for RNA-Seq where reads are mapped across long splice junctions. Lance, from your tool's help it sounds like it needs a genome database build filled in. I don't understand this requirement - Brad's tool works just fine for standalone BAM files (for example reads mapped to an in house assembly). Is that not supported in your tool? Galaxy team - why does the ToolShed allow duplicate repository names (here bam_to_bigwig) AND duplicate tool IDs (again, here bam_to_bigwig)? Won't this cause chaos when sharing workflows? I would suggest checking this when a tool is uploaded and rejecting repository name or tool ID clashes. Regards, Peter P.S. Brad, your tool is missing an explicit <requirements> tag listing the UCSC binary wigToBigWig, and the Python library pysam. Lance, your tool doesn't seem to include any author information like your name or email address. I'm inferring it is yours from the Galaxy tool shed user id, lparsons. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/