Question: How To Count Reads In 200Bp Windows And Save The Output Per Chromosome?
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gravatar for Di Nguyen
7.0 years ago by
Di Nguyen50
Di Nguyen50 wrote:
Hi all, I recently have some Gro-seq data. What I want to do is this: 1. Workflow Counting how many reads per 200bp windows per chromosome. For this, my work flow is as followed: fasq -> fasq groomer -> bowtie -> BAM to SAM -> interval BED -> 200 bp windows regional variation -> feature 2. Questions: how do I sort and save per chromosome? For example, I would like to compare X chromosome versus autosomes or X versus chromosome 1? Please accept my appreciation, Di Nguyen, U of Washington, WA
alignment bowtie • 1.1k views
ADD COMMENTlink modified 7.0 years ago by Jennifer Hillman Jackson25k • written 7.0 years ago by Di Nguyen50
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gravatar for Jennifer Hillman Jackson
7.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hello Di Nguyen, The output of the "Feature coverage" tool is a tab-delimited file, so it will work with many of the tools in Statistics, Join, Subtract and Group, Filter and Sort, and Text Manipulation plus others. "Subtract and Group -> Group" may be a good place to start. Please see the screencast "Tool tutorials -> Grouping" for an example about how to use the tool: http://galaxyproject.org/wiki/Learn/Screencasts Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
ADD COMMENTlink written 7.0 years ago by Jennifer Hillman Jackson25k
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gravatar for Jennifer Hillman Jackson
7.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hello Di, Yes, the 200 bp windows should be for the reference genome, apologies if that was not clear. The idea is to create a simple text file of the chrom-start-stop (one line per chromosome), upload, convert to BED, then create windows. Or better and less manually, you can extract the "chromInfo" table from the UCSC Table Browser (since you are using mm9, sourced from UCSC), do a few text edits to format, and use that as the BED file to create windows. Once you have the 200 bp windows as the "target ranges" for the regional variation tool, compare your "query alignments" (BAM/SAM->Interval dataset) to get coverage. Group per window, per chrom, or however you wish with the tools I mentioned. If using "Group", the other data points are the numbers that can be graphed or manipulated. But that is just one suggestions, once you have the data in the right format (tabular), trying out different tools should be quick to do and tune/evaluate. Good luck with the project, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
ADD COMMENTlink written 7.0 years ago by Jennifer Hillman Jackson25k
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