Hi Gabriel,

SAM format is just tabular data- so you could assign that as a datatype (use the pencil icon). The only concern here would be the size of the files - Excel can be easily swapped with very large files.


Converting SAM->interval is another option, if you just need the coordinates. This can also be set as "tabular" format for Excel

For both, make sure the file ends in ".tab" not ".tabular" and possibly just "txt", once downloaded, in order for Excel to recognize it (as far as I know).

Galaxy will perform many of the calculations that Excel will do (see group "Text manipulations" & others tools like "Group" or those in "Statistics", but you have likely already seen those.

Best!

Jen
Galaxy team


On 10/14/13 11:13 AM, Gabriel Calvin wrote:
Thanks for the responses It appears these programs require some background in Python or R. Is there a less code-intensive way to manipulate a sam or bam into a format viewable in Excel? Does Galaxy provide a tool for this?

If it simply is a matter of learning code, so be it.


On Fri, Oct 11, 2013 at 3:20 PM, Gabriel Calvin <gac4...@gmail.com <mailto:gac4...@gmail.com>> wrote:

    The organism is fruit fly. The piRNA reference sequence was
    obtained from http://www.fruitfly.org/p_disrupt/TE.html as
    FASTA.FORMAT.v9.4.1.

    I will check out those programs.

    Gabriel




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