Question: Table With Gene Count Reads
0
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Mike,
SAM datasets can be used as tabular data with the Text manipulation,
Filter and Sort, Join, Subtract and Group, etc. if the headers are
removed and the datatype changed. Or, you can convert the format to
Interval. For the simplest count directly on the SAM/BAM format
itself,
the tool group "NGS: SAM Tools" and "NGS: Picard (beta)" have options.
There is no "score" value from a SAM file - perhaps the reply below
was
misinterpreted? The score was derived from a GTF file, the GTF file
and
an Interval file were joined, then some summaries were created with
the
"Group" function.
The Tool Shed has a repository for the DESeq package. The instructions
explain how to prepare the inputs. "NGS: Picard (beta)" also has tools
for assigning read groups if you need to do that.
http://getgalaxy.org
http://toolshed.g2.bx.psu.edu/ Search for: DESeq
Hopefully this helps!
Jen
Galaxy team
--
Jennifer Jackson
http://galaxyproject.org