Example sam file download

This allows access to reads to be done more efficiently. To sort a BAM file: samtools sort -m file. After that, run the following command to make a BAM index: samtools index sorted. Using BEDtools to perform basic analysis tasks BEDtools is a powerful suite of tools that enables you to perform several different types of analysis. In many ways, it's like HOMER in that it is flexible and allows you to analyze your data in many different ways.

After that, move into the new directory and type "make" to compile the program: tar zxvf BEDTools. To build a density graph of your reads across the genome, use the BEDtools program " genomeCoverageBed " to create a bedGraph file. It's also a good idea to gzip file file after creating it to reduce upload times to UCSC. Can't figure something out? Click the module link to open the textbook for instructions.

If needed, you can click specific files to download—for example, to download your original start file again. You can also upload your in-progress work to SAM so that you can finish working on your project later or from a different computer. After uploading your final project files, click Submit in the Submit for Grade panel to submit your work.

If the project can't be submitted, correct the listed problem and upload the project again. For details, see Project Errors. To see your graded project for your most recent attempt, click Grading Report under Attempt History. You can go through the code to get an idea of what information it looks for to validate the file. Login before adding your answer.

Use of this site constitutes acceptance of our User Agreement and Privacy Policy. Log In. Log In Sign Up About. Small SAM Examples.

Entering edit mode.