If -bcfile is not specified all the cell barcodes will be included.Ĭell barcodes should be specified in the bcfile as the `CB` tag for each read b, -bcfile FILE Valid barcodes file, to filter the bam. Runs the velocity analysis outputting a loom file įor example if we want to run the pipeline on the cellranger output folder mypath/sample01.

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 ) - help Show this message and exit. gtf file containing intervals to mask - l, - logic TEXT The logic to use for the filtering ( default : Default ) - M, - multimap Consider not unique mappings ( not reccomended ), - samtools - threads INTEGER The number of threads to use to sort the bam by cellID file using samtools - samtools - memory INTEGER The number of MB used for every thread by samtools to sort the bam file - t, - dtype TEXT The dtype of the loom file layers - if more than 6000 molecules / reads per gene per cell are expected set uint32 to avoid truncation ( default run_10x : uint16 ) - d, - dump TEXT For debugging purposes only : it will dump a molecular mapping report to hdf5. Usage : velocyto run10x SAMPLEFOLDER GTFFILE Runs the velocity analysis for a Chromium 10 X Sample 10 XSAMPLEFOLDER specifies the cellranger sample folder GTFFILE genome annotation file Options : - s, - metadatatable FILE Table containing metadata of the various samples ( csv fortmated rows are samples and cols are entries ) - m, - mask FILE. If you are interested in running velocyto with only one technique you can directly jump to that section without loss of information (this also means that some of the information will be repeated). We will now describe the use of the technique specific subcommands. Please regard these subcommands as the recommended and easiest way to run velocyto, especially if you are unsure of all the options to pass to velocyto run.įor more flexibility and advanced usage, velocyto run should be used directly.įurthermore, to adapt velocyto to custom/new techniques the user may want to consider modification of the counting pipeline, this does not require deep rewrite of the internals but just the creation of a new logic, for more information consult the section about the Logic interface API. They take care of passing the appropriate options for each technology furthermore they performa a minimal check the inputs provided make sense and some of them infer the path of some of the input files. These subcommands are just wrappers of the main command velocyto run. The currently available are: run10x, run_smartseq2, run_dropest

However, for some of the most commonly used scRNA-seq chemistries, we provide a set of ready-to-use subcommands.

The general purpose command to run the read counting pipeline is velocyto run.

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