Question: Re: Pilup File And Counting Reads In 200Bp Windows
gravatar for Jennifer Hillman Jackson
7.2 years ago by
United States
Jennifer Hillman Jackson25k 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
galaxy • 650 views
ADD COMMENTlink written 7.2 years ago by Jennifer Hillman Jackson25k
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