Up: Component summary
Up: Component summary
Component
AligFilterMatchesAllows filtering of alignments in BAM/SAM files, mainly output from Tophat
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | |
| Authors | Alejandra Cervera (alejandra.cervera@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | samtools ; installer (bash) |
| Source files | component.xml aligFilter.sh |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| accepted_hits | BAM | Mandatory | The aligned RNA-seq reads in BAM format. |
Outputs| Name | Type | Description |
|---|---|---|
| dataOut1 | SAM | A SAM file filtered. |
| dataOut2 | SAM | A SAM file filtered. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| cutoff | int | 1 | The maximum number of alignments for each read wanted in the output. |
Test cases| Test case | Parameters▼ | IN accepted_hits |
OUT dataOut1 |
OUT dataOut2 |
||
|---|---|---|---|---|---|---|
| case1 | properties | accepted_hits | (missing) | (missing) | ||
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# Testing AligFilterMatches component, |
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