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




--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
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