kallisto/kallisto_quant
kallisto
quant
pseudoalignment
Description
Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
Input
Name | Type & Properties | Description |
|---|---|---|
--input | file required multiple | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. |
--index -i | file required | Kallisto genome index. |
Output
Name | Type & Properties | Description |
|---|---|---|
--output_dir -o | file required output | Directory to write output to. |
--log | file output | File containing log information from running kallisto quant |
Options
Name | Type & Properties | Description |
|---|---|---|
--single | boolean_true | Single end mode. |
--single_overhang | boolean_true | Include reads where unobserved rest of fragment is predicted to lie outside a transcript. |
--fr_stranded | boolean_true | Strand specific reads, first read forward. |
--rf_stranded | boolean_true | Strand specific reads, first read reverse. |
--fragment_length -l | double | The estimated average fragment length. |
--sd -s | double | The estimated standard deviation of the fragment length (default: -l, -s values are estimated from paired end data, but are required when using --single). |
--plaintext | boolean_true | Output plaintext instead of HDF5. |
--bootstrap_samples -b | integer | Number of bootstrap samples to draw. Default: '0' |
--seed | integer | Random seed for bootstrap. Default: '42' |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output_dir: "$id.$key.output_dir"
log: "$id.$key.log"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/biobox.git \
-revision v0.3.1 \
-main-script target/nextflow/kallisto/kallisto_quant/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
kallisto/kallisto_quantbiobox v0.3.1
Uses
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