FAQ#501 Version4
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Can I upload 3' adapter clipped input files?
| Category: | smallRNA Pipeline | Difficluty: |  |
| Assigned to: | - | Due date: | |
| Related issue: | - | Related Message: | - |
| Related version: | - | Valid: | Valid |
Answer
Yes, the pipeline accepts 3' adapter clipped input files.
- If your 3' adapter sequence is clipped, then you should choose the "NO 3' ADAPTER (already removed from these reads)" option in the "3' Adapter Sequence Options" section.
- If your 3' adapter sequence is NOT clipped, then follow the directions below:
- If you know the 3' adapter sequence for your sample(s), it is highly recommended to provide that adapter sequence by choosing the "MANUALLY SPECIFY 3' ADAPTER" option and then typing your adapter sequence in the "Manual Input of 3' Adapter Sequence" text box.
- However, by default, the pipeline will attempt to find your 3' adapter sequence and remove it from your sample(s), so you are not required to provide your 3' adapter sequence or clip your 3' adapter sequence beforehand.