bedtools/bedtools_bamtofastq
Conversion
BAM
FASTQ
Description
Convert BAM alignments to FASTQ files.
This tool extracts FASTQ records from sequence alignments in BAM format,
supporting both single-end and paired-end data extraction.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input -i | file required | Input BAM file to be converted to FASTQ. **Requirements:** - Must be in BAM format - For paired-end output, should be sorted by query name |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--fastq -fq | file required output | Output FASTQ file for single-end data or first mate in paired-end data. **Output format:** Standard FASTQ format with sequence and quality scores |
--fastq2 -fq2 | file output | Output FASTQ file for second mate in paired-end data. **Usage:** - Required only for paired-end BAM files - BAM should be sorted by query name for proper pairing - If omitted, only first mates or single-end reads are extracted |
Options
Name | Type & Properties | Description |
|---|---|---|
--tags | boolean_true | Create FASTQ based on mate information in BAM R2 and Q2 tags. **Usage:** - Uses R2 tag for second mate sequence - Uses Q2 tag for second mate quality scores - Alternative to requiring coordinate-sorted paired BAM |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
fastq: "$id.$key.fastq.fastq"
fastq2: "$id.$key.fastq2.fastq"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/biobox.git \
-revision v0.4.0 \
-main-script target/nextflow/bedtools/bedtools_bamtofastq/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
bedtools/bedtools_bamtofastqbiobox v0.4.0
Uses
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