Update Tutorial_20221025.md

chenweng1991 · Oct 27, 2022 · cbc9394 · cbc9394
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commit cbc9394
Showing 1 changed file with 41 additions and 2 deletions.
diff --git a/Tutorial_20221025.md b/Tutorial_20221025.md
@@ -77,7 +77,12 @@ multiqc fastqc
 ```console
 $MyMultiome/MultiomeATAC_mito.sh -n Tutorial_Mito -1 Example.R1.fq.gz -2 Example.R2.fq.gz -i Example.i5.fq.gz -c 0 -t 8 -m $MyMultiome -b Genome/hg38.mitoMask  # add -q for quick, which skip the QC steps
 ```
+After this step a QCplot is generated
+![Old1_HSPC_Mito QCplot](https://user-images.githubusercontent.com/43254272/198318936-1c7f1f4b-c203-4b93-8997-b1d82adc3b62.png)
+
 ## Step3: Parse the Cellranger qualified cell barcode
+In a ReDeeM experiment, the ATAC and RNA data is analyzed by Cellranger arc. The barcodes.tsv.gz from that will be parsed here.
+Becasue the barcode in barcodes.tsv.gz is RNA barcode, we need to translate into ATAC barcode (via RNAbc2ATAC.R) to be able to match mtDNA data
 ```console
 ln -s $REDEEM_V/source/barcodes.tsv.gz ./
 Rscript $MyMultiome/Helpers/RNAbc2ATAC.R barcodes.tsv.gz Tutorial_atac.barcodes.tsv
@@ -104,6 +109,40 @@ $mitoConsensus/Finalize.sh $WD $Threads $mitoConsensus
 
 # Expected result
 - Location: The results are saved in $WD/final
-- Major 5 files: QualifiedTotalCts, RawGenotypes.Total.StrandBalance(Least stringent), RawGenotypes.VerySensitive.StrandBalance, RawGenotypes.Sensitive.StrandBalance, RawGenotypes.Specific.StrandBalance (Most Stringent)
+- Major 5 files: 
+  - QualifiedTotalCts, 
+  - RawGenotypes.Total.StrandBalance(Least stringent), 
+  - RawGenotypes.VerySensitive.StrandBalance(Less stringent), 
+  - RawGenotypes.Sensitive.StrandBalance(Stringent), 
+  - RawGenotypes.Specific.StrandBalance (Most Stringent)
+- QualifiedTotalCts is a table with 6 columnes that show mtDNA coverage per position per cell
+
+| Cellbarcode| coordinates on mt genome|# unique frag(total)|# unique frag(less stringent)|# unique frag(stringent)|# unique frag(very stringent)|
+| ------------- |----------------------|--------------------|-----------------------------|------------------------|-----------------------------|
+
+- RawGenotypes is a table with 14 columnes that show the consensus variant calling.  Each row is a molecule with a potential variant
+
+|MoleculeID | CellBC | Pos | Variant | V | Ref | FamSize | V-counts | CSS | DB_Cts | SG_Cts | Is+ | Is- | TotalDepth|
+|-----------|--------|-----|--------|---------|----------|---------|---------|-----|--------|---------|-----|-----|-----------|
+
+1. MoleculeID: Cellbarcode+start+end which is the identifier to define a molecule
+2. CellBC: Cell barcode
+3. Pos: The coordinate of the variant
+4. Variant: A description of the variant
+5. V: The variant base called on Pos
+6. Ref: The reference base on Pos
+7. FamSize: The consensus family size, or the total number of PCR copies for the given molecule
+8. V-count: Number of PCR copies that support the variant
+9. CSS: Consensus score, which is the proportion of PCR copies that support the variant
+10. DB_Cts: Number of double cover copies, which are positions that sequenced by both Read1 and Read2
+11. SG_Cts: Number of single cover copies, which are positions that sequenced by only Read1 or Read2
+12. Is+: If the variant is discovered on plus strand
+13. Is- : If the variant is discovered on minus strand
+14. TotalDepth: On this given position, total number of unique fragment in the given cell
+
+- Strand biased variant has been removed 
+![StrandBiase](https://user-images.githubusercontent.com/43254272/198328824-40977739-6fdf-4813-9461-9c5bee18d53a.png)
+
 - QualifiedTotalCts and RawGenotypes.* are the inputs for REDEEM-R for downstream mutation filtering and phylogenetic tree reconstruction
-- 
+
+