Question: Bootstrap value in kallisto
0
gravatar for sg927357
10 weeks ago by
sg9273570
sg9273570 wrote:

What is the default parameter of bootstrap value in kallisto tool at the quantification stage???What should be a good bootstrap value for rna-seq data?

kallisto • 176 views
ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by sg9273570

Thanks for the information

ADD REPLYlink written 10 weeks ago by sg9273570
3
gravatar for Kevin Blighe
10 weeks ago by
Kevin Blighe51k
Kevin Blighe51k wrote:

The information is right there..

kallisto quant
kallisto 0.44.0
Computes equivalence classes for reads and quantifies abundances

Usage: kallisto quant [arguments] FASTQ-files

Required arguments:
-i, --index=STRING            Filename for the kallisto index to be used for
                              quantification
-o, --output-dir=STRING       Directory to write output to

Optional arguments:
    --bias                    Perform sequence based bias correction
-b, --bootstrap-samples=INT   Number of bootstrap samples (default: 0)
    --seed=INT                Seed for the bootstrap sampling (default: 42)
    --plaintext               Output plaintext instead of HDF5
    --fusion                  Search for fusions for Pizzly
    --single                  Quantify single-end reads
    --single-overhang         Include reads where unobserved rest of fragment is
                              predicted to lie outside a transcript
    --fr-stranded             Strand specific reads, first read forward
    --rf-stranded             Strand specific reads, first read reverse
-l, --fragment-length=DOUBLE  Estimated average fragment length
-s, --sd=DOUBLE               Estimated standard deviation of fragment length
                              (default: -l, -s values are estimated from paired
                               end data, but are required when using --single)
-t, --threads=INT             Number of threads to use (default: 1)
    --pseudobam               Save pseudoalignments to transcriptome to BAM file
    --genomebam               Project pseudoalignments to genome sorted BAM file
-g, --gtf                     GTF file for transcriptome information
                              (required for --genomebam)
-c, --chromosomes             Tab separated file with chrosome names and lengths
                              (optional for --genomebam, but recommended)

There is no correct or incorrect value to use. When I use Kallisto, I default to 50 bootstraps.

Note that the bootstrapped values are then output to the abundance.h5 file.

Kevin

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by Kevin Blighe51k
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