velocyto CLI

Requirements on the input files

velocyto assumes that the bam file that is passed to the CLI contains a set of information and that some upstream analysis was performed on them already. In particular the bam file will have to:

Be sorted by mapping position. Represents either a single sample (multiple cells prepared using a certain barcode set in a single experiment) or single cell. Contain an error corrected cell barcodes as a TAG named CB or XC. Contain an error corrected molecular barcodes as a TAG named UB or XM.

Note

For SmartSeq2 bam files (3) and (4) are not required because it consists of one bam file per cell and no umi are present.

velocyto assumes that the gtf file follows the GENCODE gtf format description. However some mandatory field are relaxed to extend compatibility to a wider set of gtf files. In particular the gtf file will have to:

Contain the 3rd column entry feature-type. Note that only the exon entry of the gtf file marked as exon in this column will be considered and therefore the requirements below only apply to the exon labeled lines. Contain, in the 9th column, the key-value pair transcript_id, containing an unique identified for the transcript model. Contain, in the 9th column, the key-value pair transcript_name (Optional, if not present it will be set to the value of transcript_id) Contain, in the 9th column, the key-value pair gene_id, containing an unique identified for the gene. Contain, in the 9th column, the key-value pair gene_name (Optional, if not present it will be set to the value of gene_id) Contain, in the 9th column, the key-value pair exon_number (Recommended but optional, if not provided velocyto will sort exons in memory and number them)