How To Count Reads In 200Bp Windows And Save The Output Per Chromosome?

Question: How To Count Reads In 200Bp Windows And Save The Output Per Chromosome?

7.2 years ago by

Di Nguyen • 50 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 • 1.2k views

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modified 7.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.2 years ago by Di Nguyen • 50

7.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 7.2 years ago by Jennifer Hillman Jackson ♦ 25k

7.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 7.2 years ago by Jennifer Hillman Jackson ♦ 25k

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