QIAseq UPX 3' Transcriptome Kit
Analysis workflow versions- v1.0 - RNA Analysis Portal 1.0, RNA-seq Analysis Portal 1.1
- v1.1 - RNA-seq Analysis Portal 2.0
- v1.2 - RNA-seq Analysis Portal 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. Version numbers such as "v1.0" refer to the analysis workflow version.
| Demultiplex Reads | |
| Allow mismatches | v1.0, v1.1: No |
| v1.2: Yes | |
| Naming | v1.0, v1.1: [row][column] (e.g. Sample1 A1, Sample1 A2) |
| v1.2: [cellID] (e.g. Sample1 C1, Sample1 C2) |
| Remove and Annotate with Unique Molecular Index | |
| Read structure | Paired end reads (Index on Read 2) |
| Number of bases to remove | 12 |
| Start position of unique molecular index | 0 |
| Length of unique molecular index | 12 |
| Trim read-through common sequence and UMI | Yes |
| - Part of insert to search for | 27 |
| - Part of common sequence and UMI to search for | 3 |
| - Number of errors allowed in match | 3 |
| Trim Reads - Trim short polyA from middle of R1, discard R2 | |
| Adapter trimming by Trim adapter list | UPX_3_prime_adapter_list |
| Discard short reads | Yes |
| - Minimum length | 15 |
| Trim Reads - Trim polyA and polyG from R1 | |
| Trim homopolymers from 3' | polyA, polyG |
| Discard short reads | Yes |
| - Minimum length | 15 |
| Create UMI Reads from Reads | |
| Read structure | Single end reads |
| Minimum UMI read length | 20 |
| Minimum average quality score | 20 |
| Minimum UMI group size | 1 |
| Set ambiguous nucleotides to N | Yes |
| Coarse grouping | |
| - Hasher type | Simple k-mer hasher |
| - k-mer length | 16 |
| - Number of hashes | 16 |
| - Similarity factor | 2 |
| Fine grouping | |
| - Hasher type | Simple k-mer hasher |
| - k-mer length | 5 |
| - Number of hashes | 16 |
| - Segment length | 40 |
| - Minimum similarity (same UMI) | 10 |
| - Minimum similarity (similar UMI) | 10 |
| Trim Reads - Trim low quality and ambiguous ends | |
| Trim using quality scores | Yes |
| - Quality limit | 0.05 |
| Trim ambiguous nucleotides | Yes |
| - Maximum number of ambiguities | 2 |
| Discard short reads | Yes |
| - Minimum length | 15 |
| 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 | 3' sequencing |
| 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 |