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 <[email protected]
<mailto:[email protected]>> 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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http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
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