Command Line Tool API

This page contains a description of all the subcomand inputs of the command line tool velocyto. For a usage guide refear to the command line tool tutorial

velocyto

velocyto [OPTIONS] COMMAND [ARGS]...

extract_intervals

Transform a genome annotation .gtf file into a intervals .txt file required to run velocyto.

GTF_FILE: input file

velocyto extract_intervals [OPTIONS] GTFFILE

Options

--dogenes, --no-dogenes

whether to process gene models [default: True]

--dotrs, --no-dotrs

whether to process transcript models [default: True]

-p, --outfileprefix <outfileprefix>

prefix to the output files [default: /home/travis/build/velocyto-team/velocyto.py/doc/intervals]

Arguments

GTFFILE

Required argument

extract_repeats

Transform a repeats .gtf file into a intervals .gtf file.

GTFFILE .gtf file with annotated repeats to mask

velocyto extract_repeats [OPTIONS] GTFFILE

Options

-t, --tolerance <tolerance>

[default: 5]

Arguments

GTFFILE

Required argument

multi10x

Runs the velocity analysis on multiple a Chromium samples in parallel, spawning several subprocesses

velocyto multi10x [OPTIONS] PARENTFOLDER IVLFILE

Options

-n, --number <number>

Number of processes to execute

-w, --wait <wait>

Delay in seconds between the executions of single run comands

-s, --metadatatable <metadatatable>

Table containing metadata of the various samples (csv fortmated, [row:samples, col:entry])

-m, --repmask <repmask>

.gtf file containing intrvals sorted by chromosome, strand, position (e.g. generated by running velocyto extract_repeats mm10_rmsk.gtf)

-z, --introns <introns>

introns validation heuristic mode. if strict if will require exon-intron spanning evidence; if permissive it does not check for spanning

-l, --logfolder <logfolder>

Folder where all the log files will be generated

-d, --debug

debug mode. It will generate .sam files of individual reads (not molecules) that are identified as exons, introns, ambiguous and chimeras

Arguments

PARENTFOLDER

Required argument

IVLFILE

Required argument

run

Runs the velocity analysis outputing a loom file

BAMFILE bam file with sorted reads

IVLFILE text file generated by velocyto extract_intervals

velocyto run [OPTIONS] BAMFILE IVLFILE

Options

-b, --bcfile <bcfile>

Valid barcodes file, to filter the bam. If –bcfile is not specified all the cell barcodes will be incuded. Cell barcodes should be specified in the bcfile as the CB tag of each read

-o, --outputfolder <outputfolder>

Output folder, does not need to exist

-e, --sampleid <sampleid>

The sample name that will be used to retrieve informations from metadatatable

-s, --metadatatable <metadatatable>

Table containing metadata of the various samples (csv fortmated, [row:samples, col:entry])

-m, --repmask <repmask>

.gtf file containing intrvals sorted by chromosome, strand, position (e.g. generated by running velocyto extract_repeats mm10_rmsk.gtf)

-z, --introns <introns>

introns validation heuristic mode. if strict if will require exon-intron spanning evidence; if permissive it does not check for spanning

-d, --debug

debug mode. It will generate .sam files of individual reads (not molecules) that are identified as exons, introns, ambiguous and chimeras

Arguments

BAMFILE

Required argument

IVLFILE

Required argument

run10x

Runs the velocity analysis for a Chromium 10X Sample

10XSAMPLEFOLDER specifies the cellranger sample folder

IVLFILE text file generated by velocyto extract_intervals

velocyto run10x [OPTIONS] SAMPLEFOLDER IVLFILE

Options

-s, --metadatatable <metadatatable>

Table containing metadata of the various samples (csv fortmated, [row:samples, col:entry])

-m, --repmask <repmask>

.gtf file containing intrvals sorted by chromosome, strand, position (e.g. generated by running velocyto extract_repeats mm10_rmsk.gtf)

-z, --introns <introns>

introns validation heuristic mode. if strict if will require exon-intron spanning evidence; if permissive it does not check for spanning

-d, --debug

debug mode. It will generate .sam files of individual reads (not molecules) that are identified as exons, introns, ambiguous and chimeras

Arguments

SAMPLEFOLDER

Required argument

IVLFILE

Required argument