Output file format
==================

gRNA_mutation
-------------

consensus.bam: Bam file contains consensus sequence alignment result for each UMI. 
consensus.sequence.gRNA.variant.txt: 
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 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 guide
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 1 – 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.


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

all.MT.txt: mutations of all in-cell guides same format as MT.txt. An important difference is multiple cells with the same variant guide will be recorded once in this file, but multiple times in MT.txt. 
consensus.sequence.gRNA.MT.txt: same format as all.MT.txt but for all mutations in consensus.sequence.gRNA.variant.txt including guides that are not detected in cells. Variants with at least 2 UMIs will be recorded. Each variant only appears once in this file.

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 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 13: mutation, ‘No mutation’ given when wildtype sequence. "Deletion at cutsite”, "Insertion/Deletion somewhere else”, "Mismatch” 
Column 14: gRNA assigned to this cell 


