Question: Table With Gene Count Reads
gravatar for Jennifer Hillman Jackson
6.3 years ago by
United States
Jennifer Hillman Jackson25k 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. Search for: DESeq Hopefully this helps! Jen Galaxy team -- Jennifer Jackson
galaxy • 737 views
ADD COMMENTlink written 6.3 years ago by Jennifer Hillman Jackson25k
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