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
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 |