Output file format

gRNA_mutation

consensus.bam: Bam file contains consensus sequence alignment result for each UMI.

consensus.sequence.gRNA.variant.txt

column number

Value

Column 1

Cell barcode

Column 2

UMI

Column 3

Number of UMI in the cell

Column 4

Number of reads for this UMI (default min = 1)

Column 5

single/multiple. Single refers to UMI with only one type of sequence. Multiple refers to UMI with more than one type of sequence.

Column 6

Consensus sequence. Sequence with most reads supported.

Column 7

Number of reads that support the consensus sequence.

Column 8

True/False. True: wild type sequence. False: different from reference.

Column 9

Name of the guide. ‘multiple gene’: when UMI mapped to multiple guides with equal number of reads. The progam cannot assign gene to UMI confidently. In this case, UMI will be skipped later.

Column 10

Guide variant type with detailed mismatch information

Column 11

Mutation structure annotation

cells.gRNA.txt

column number

Value

Column 1

Cell barcode

Column 2

Number of guides in the cell

Column 3

Guide name.

Column 4

WT: Intact gRNA

Column 5

Number of UMI support wild type guide

Column 6

Guide variant type if exist.

Column 7

Number of UMI support mutant guide.

cells.gRNA.single.txt: cells with only one gRNA

column number

Value

Column 1

Cell barcode

Column 2

1 as only one guide in the cell

Column 3

Guide name. Guide name ends with WT represents wild type.

Column 4

Number of UMI support mutant guide.

cells.gRNA.single.MT.txt

column number

Value

Column 1 to Column 4

same as cells.gRNA.single.txt

Column 5

Mutation details. None when wildtype or soft clipping only.

Column 6

Mutant sequence. None when wildtype or soft clipping only.

all.MT.txt: mutations in single cell in a long format, each line contains single mutation event.

column number

Value

Column 1

target gene

Column 2

structure (defined in structure.gtf)

Column 3

length of the structure

Column 4

Position on the structure

Column 5

mutation (CIGAR similar format)

Column 6

variant name with number suffix.

editing_effect

For each gRNA: {region_name}.bam: alignment within detection window {region_name}.bam.featureCounts.sorted.bam: FeatureCount assigned reads to gene. {region_name}.consensus.sequence.txt: Consensus sequence within detection window for each UMI and cell.

column number

Value

Column 1

cell barcode

Column 2

UMI

Column 3

Number of UMI for cell

Column 4

Number of sequences for that UMI

Column 5

reference sequence in the detection window

Column 6

union sequence for that UMI in the detection window

Column 7

union number of reads

Column 8

Boolean True for wildtype sequence, false for mutation exist in sequence

Column 9

mapped gene

Column 10

mapped positions on the genome

Column 11

is_umi_seq_different

Column 12

reference gRNA id (region_name)

{region_name}.editing_effect.cutsite.txt

column number

Value

Column 1 to Column 12

same as {region_name}.consensus.sequence.txt

Column 13

mutation, ‘No mutation’ given when wildtype sequence. “Deletion at cutsite”, “Insertion/Deletion somewhere else”, “Mismatch”

Column 14

gRNA assigned to this cell