[galaxy-user] Pilup file and counting reads in 200bp windows

[Jennifer Jackson]

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