Hello Di,
Once the data is in pile-up format, the read identifier is lost, so summarizing per-read over a range is not possible.
However, you could graph the data, which would graph the number of reads represented per reference genome position. Do this with "Graph/Display Data -> Histogram", on the pileup coverage value and setting the number of breaks per chromosome so that they end up being each ~200 bases.
Or, going back to the BAM/SAM data, the tool "Regional Variation -> Make windows" can create 200 bp windows per chromosome (given an input BED3 file - chrom, start, end). Then use this and the BAM/SAM alignments (converted to interval) as input for the tool "Regional Variation -> Feature coverage".
Hopefully one of the options will work for you,
Best, Jen Galaxy team
ps. Please send all questions directly to the mailing lists unless they contain private data/links.
On 10/4/11 3:18 PM, Di Nguyen wrote:
Hi Jennifer,
I have some Chip seq data that I can map with bwa, then I can generate a pileup file. My question is how do we count how many reads in a 200bp windows, say for Chromosome X or autosomes? Please help!
My utmost appreciation,
Di Nguyen UWashington