[galaxy-user] Pilup file and counting reads in 200bp windows
jen at bx.psu.edu
Tue Oct 4 19:39:55 EDT 2011
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 ->
Hopefully one of the options will work for you,
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
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