Question: Re: Pilup File And Counting Reads In 200Bp Windows
0
Jennifer Hillman Jackson ♦ 25k wrote:
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.
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support