Workflow from UCSC genes and symbols


StepAnnotation
Step 1: Input dataset
select at runtime
Table mapping gene ids from BED file into names suitable for downstream analysis
Step 2: Input dataset
select at runtime
Genes to match against in BED format
Step 3: Input dataset
select at runtime
Your features of interest in BED format **must be 3 exactly columns**
Step 4: Join
Output dataset 'output' from step 3
Output dataset 'output' from step 2
1
Only records that are joined (INNER JOIN)
Step 5: Subtract
Output dataset 'output' from step 4
Output dataset 'output' from step 3
Intervals with no overlap
1
Step 6: Join two Datasets
Output dataset 'output' from step 4
7
Output dataset 'output' from step 1
1
No
No
No
No

No value found for 'Keep the header lines'. Using default: ''.

Step 7: Fetch closest non-overlapping feature
Output dataset 'output' from step 5
Output dataset 'output' from step 2
Either Upstream or Downstream
Step 8: Count
Output dataset 'out_file1' from step 6
17
Tab
By the values being counted

No value found for 'How should the results be sorted?'. Using default: 'value'.

Step 9: Join two Datasets
Output dataset 'out_file1' from step 7
7
Output dataset 'output' from step 1
1
No
No
No
No

No value found for 'Keep the header lines'. Using default: ''.

Step 10: Cut
c2
Tab
Output dataset 'out_file1' from step 8
Step 11: Count
Output dataset 'out_file1' from step 9
17
Tab
By the values being counted

No value found for 'How should the results be sorted?'. Using default: 'value'.

Step 12: Cut
c2
Tab
Output dataset 'out_file1' from step 11