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 |