Command Line Tool API

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

velocyto

velocyto [OPTIONS] COMMAND [ARGS]...

Options

--version

Show the version and exit.

run

Runs the velocity analysis outputing a loom file

BAMFILE bam file with sorted reads

GTFFILE genome annotation file

velocyto run [OPTIONS] BAMFILE... GTFFILE

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 for each read

-o, --outputfolder <outputfolder>

Output folder, if it does not exist it will be created.

-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 formatted, rows are samples and cols are entries)

-m, --mask <mask>

.gtf file containing intervals to mask

-c, --onefilepercell

If this flag is used every bamfile passed is interpreted as an independent cell, otherwise multiple files are interpreted as batch of different cells to be analized together. Important: cells reads should not be distributed over multiple bamfiles is not supported!! (default: off)

-l, --logic <logic>

The logic to use for the filtering (default: Default)

-U, --without-umi

If this flag is used the data is assumed UMI-less and reads are counted instead of molecules (default: off)

-u, --umi-extension <umi_extension>

In case UMI is too short to guarantee uniqueness (without information from the ampping) set this parameter to chr, Gene ro [N]bp If set to chr the mapping position (binned to 10Gb intervals) will be appended to UB (ideal for InDrops+dropEst). If set to Gene then the GX tag will be appended to the UB tag. If set to [N]bp the first N bases of the sequence will be used to extend UB (ideal for STRT). (Default: no)

-M, --multimap

Consider not unique mappings (not reccomended)

-@, --samtools-threads <samtools_threads>

The number of threads to use to sort the bam by cellID file using samtools

--samtools-memory <samtools_memory>

The number of MB used for every thread by samtools to sort the bam file

-d, --dump <dump>

For debugging purposes only: it will dump a molecular mapping report to hdf5. –dump N, saves a cell every N cells. If p is prepended a more complete (but huge) pickle report is printed (default: 0)

-v, --verbose

Set the vebosity level: -v (only warinings) -vv (warinings and info) -vvv (warinings, info and debug)

Arguments

BAMFILE

Required argument(s)

GTFFILE

Required argument

run-dropest

Runs the velocity analysis on DropEst preprocessed data

BAMFILE bam files to be analyzed

GTFFILE genome annotation file

velocyto run-dropest [OPTIONS] BAMFILE GTFFILE

Options

-b, --bcfile <bcfile>

Valid barcodes file, to filter the bam. If –bcfile is not specified the file will be searched in the default position outputed by velocyto tools dropest_bc_correct. Otherwise an error will be thrown

-l, --logic <logic>

The logic to use for the filtering (default: Default)

-o, --outputfolder <outputfolder>

Output folder, if it does not exist it will be created.

-e, --sampleid <sampleid>

The sample name that will be used as a the filename of the output.

-m, --repmask <repmask>

.gtf file containing intervals to mask (Optional)

-@, --samtools-threads <samtools_threads>

The number of threads to use to sort the bam by cellID file using samtools

--samtools-memory <samtools_memory>

The number of MB used for every thread by samtools to sort the bam file

-d, --dump <dump>

For debugging purposes only: it will dump a molecular mapping report to hdf5. –dump N, saves a cell every N cells. If p is prepended a more complete (but huge) pickle report is printed (default: 0)

-v, --verbose

Set the vebosity level: -v (only warinings) -vv (warinings and info) -vvv (warinings, info and debug)

Arguments

BAMFILE

Required argument

GTFFILE

Required argument

run-smartseq2

Runs the velocity analysis on SmartSeq2 data (independent bam file per cell)

[BAMFILES, …] a sequence of bam files to be analyzed (e.g. use a wild-card expansion)

GTFFILE genome annotation file

velocyto run-smartseq2 [OPTIONS] BAMFILES... GTFFILE

Options

-o, --outputfolder <outputfolder>

Output folder, if it does not exist it will be created.

-e, --sampleid <sampleid>

The sample name that will be used as a the filename of the output.

-m, --repmask <repmask>

.gtf file containing intervals to mask

-d, --dump <dump>

For debugging purposes only: it will dump a molecular mapping report to hdf5. –dump N, saves a cell every N cells. If p is prepended a more complete (but huge) pickle report is printed (default: 0)

-v, --verbose

Set the vebosity level: -v (only warinings) -vv (warinings and info) -vvv (warinings, info and debug)

Arguments

BAMFILES

Required argument(s)

GTFFILE

Required argument

run10x

Runs the velocity analysis for a Chromium 10X Sample

10XSAMPLEFOLDER specifies the cellranger sample folder

GTFFILE genome annotation file

velocyto run10x [OPTIONS] SAMPLEFOLDER GTFFILE

Options

-s, --metadatatable <metadatatable>

Table containing metadata of the various samples (csv fortmated rows are samples and cols are entries)

-m, --mask <mask>

.gtf file containing intervals to mask

-l, --logic <logic>

The logic to use for the filtering (default: Default)

-M, --multimap

Consider not unique mappings (not reccomended)

-@, --samtools-threads <samtools_threads>

The number of threads to use to sort the bam by cellID file using samtools

--samtools-memory <samtools_memory>

The number of MB used for every thread by samtools to sort the bam file

-d, --dump <dump>

For debugging purposes only: it will dump a molecular mapping report to hdf5. –dump N, saves a cell every N cells. If p is prepended a more complete (but huge) pickle report is printed (default: 0)

-v, --verbose

Set the vebosity level: -v (only warinings) -vv (warinings and info) -vvv (warinings, info and debug)

Arguments

SAMPLEFOLDER

Required argument

GTFFILE

Required argument

tools

helper tools for velocyto

velocyto tools [OPTIONS] COMMAND [ARGS]...

dropest-bc-correct

Using the output of DropEst: (1) Corrects barcodes directly in the bam file (2) Produces a valid barcodes list

BAMFILEPATH - bam file with sorted reads obtained running DropEst

DROPEST-OUT - R dump rds file generated by DropEst

velocyto tools dropest-bc-correct [OPTIONS] BAMFILEPATH DROPEST_OUT

Options

-o, --corrected-output <corrected_output>

(Optional) The file output of the output bam file. Otherwise the file will be outputed in the same folder of the input with the prefix correct_

Arguments

BAMFILEPATH

Required argument

DROPEST_OUT

Required argument