zUMIs-config: Generate yaml file

Name of the run/project:

Path to the output directory:

Input options:

Number of input fastq files:

Search for sequence pattern in reads?

Correct for frameshift in barcode reads?

In this section, fill only those fields that fit your input files:

Mapping/Reference options:

Full path to the STAR index directory:

Full path to the annotation GTF file:

Optional: Additional mapping parameters for STAR:

Optional: Number of additional reference sequences:

Additional references:

General options:

Number of CPU Threads:

Memory limit (Gb) 0 = no limit:

Produce summary statistics

Start zUMIs from following stage:

Barcode & UMI filtering options:

Number of barcode bases below quality:

Barcode Phred quality threshold:

Number of UMI bases below quality:

UMI Phred quality threshold:

Counting options:

Generate intron & exon+intron count tables?

Number of reads to downsample to:

Is the library stranded?

Hamming distance collapsing of UMI sequences:

Generate RNA velocity counting of intron-exon spanning reads. Assumes velocyto is installed in path.

Count the primary Hits of multimapping reads towards gene expression levels?

Perform STAR twoPass mapping?

Barcode options:

Type of barcode selection:

Automatic

Number of top Barcodes

Barcode whitelist

Hamming distance collapsing of close cell barcode sequences.

Keep only the cell barcodes with atleast n number of reads

Dependencies:

Rscript executable:

samtools executable:

pigz executable:

STAR executable:

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