Up: Component summary
Up: Component summary
Component
Bam2FastqRevert BAM file to Fastq file for realignment. Requires Samtools and Picard to run from PATH.
| Version | 0.1 |
|---|---|
| Bundle | sequencing |
| Categories | Convert smallRNA |
| Authors | Katherine Icay (katherine.icay@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | samtools ; picard ; installer (bash) |
| Source files | component.xml Bam2Fastq.sh |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| in | BAM | Mandatory | Input BAM alignment file. |
Outputs| Name | Type | Description |
|---|---|---|
| out | FASTQ | Output FASTQ file. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| picard | string | "../../lib/picard-tools-1.131" | Path to picard installation. |
Test cases| Test case | Parameters▼ | IN in |
OUT out |
|---|---|---|---|
| case1 | (missing) | in | out |