QIAseq UPXome RNA Lib Kit (N6-T + ODT-T RT primers)
Analysis workflow versions- v1.0 - RNA-seq Analysis Portal 3.0.1, 4.0, 4.1, 5.0
Analysis workflow parameters
Only applied options and parameter are listed.
Analysis workflow section A
| Demultiplex Reads | |
| Allow mismatches | Yes |
| Naming | [row][column, padded to two digits] |
| (e.g. Sample1 A01, Sample1 A10, Sample1 C07) |
| Trim Reads; adapter trim | |
| Automatic read-through adapter trimming | Yes |
| Remove 16 bases from Read 2 5'end (adapter) | Yes |
Analysis workflow section B1 (Gene expression)
| Trim Reads; quality and ambiguity trim | |
| Trim using quality scores | Yes |
| - Quality limit | 0.05 |
| Trim ambiguous nucleotides | Yes |
| - Maximum number of ambiguities | 2 |
| Automatic read-through adapter trimming | Yes |
| Trim homopolymers from 3' | PolyA, PolyG, PolyT |
| Discard short reads | Yes |
| RNA-Seq Analysis | |
| Mismatch cost | 2 |
| Insertion cost | 3 |
| Deletion cost | 3 |
| Length fraction | 0.8 |
| Similarity fraction | 0.8 |
| Auto-detect paired distances | No |
| Maximum number of hits for a read | 10 |
| Strand specific | Reverse |
| Library type | Bulk |
| Ignore broken pairs | Yes |
| Expression value | Total counts |
Analysis workflow section B2 (Transcript expression)
| Trim Reads; extract N6-T reads | |
| Discard reads with ODT-T primer | Yes |
| Trim Reads; quality and ambiguity trim | |
| Trim using quality scores | Yes |
| - Quality limit | 0.05 |
| Trim ambiguous nucleotides | Yes |
| - Maximum number of ambiguities | 2 |
| Automatic read-through adapter trimming | Yes |
| Trim homopolymers from 3' | PolyA, PolyG, PolyT |
| Discard short reads | Yes |
| RNA-Seq Analysis | |
| Mismatch cost | 3 |
| Insertion cost | 3 |
| Deletion cost | 3 |
| Length fraction | 0.4 |
| Similarity fraction | 0.9 |
| Auto-detect paired distances | No |
| Maximum number of hits for a read | 10 |
| Strand specific | Reverse |
| 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 |