Collibri Stranded RNA Library Prep Kit for Illumina Systems
Analysis workflow versions- v1.0 - RNA-seq Analysis Portal 1.1
- v1.1 - RNA-seq Analysis Portal 2.0, 2.5, 3.0, 3.0.1, 4.0, 4.1, 5.0, 5.1
Analysis workflow parameters
Only applied options and parameter are listed.
| Trim Reads | |
| Trim using quality scores | Yes |
| - Quality limit | 0.05 |
| Trim ambiguous nucleotides | Yes |
| - Maximum number of ambiguities | 2 |
| Automatic read-through adapter trimming | Yes |
| Adapter trimming by Trim adapter list | TruSeq adapters |
| Trim homopolymers from 3' | PolyG |
| RNA-Seq Analysis | |
| Mismatch cost | 2 |
| Insertion cost | 3 |
| Deletion cost | 3 |
| Length fraction | 0.8 |
| Similarity fraction | 0.8 |
| Auto-detect paired distances | Yes |
| Maximum number of hits for a read | 10 |
| Strand specific | Forward |
| Library type | Bulk |
| Ignore broken pairs | Yes |
| Expression value | Total counts |
Create experiment analysis workflow parameters
Only applied options and parameter are listed.
| Differential Expression for RNA-Seq | |
| Technology | Whole transcriptome RNA-Seq |
| Normalization method | TMM |
| Filter on average expression for FDR correction | Yes |
| Create Heat Map for RNA-Seq | |
| Distance measure | Euclidean distance |
| Linkage criteria | Complete linkage |