What are the definitions of the Deep Sequence QC metrics in the Arima SV pipeline?
- HiC QC: If % INTRA > 15kb is > 25% a sample passes HiC QC
- SV QC: If the % INTRA > 15kb is > 25% and the Lcis/trans ratio is > 1 a samples passes SV QC
- Sample Name: Sample name
- Raw PE reads: Raw # of read pairs
- Mapped SE reads: # of single-end reads that can be mapped to the reference
- %_Mapped SE_reads: % of single-end reads that can be mapped to the reference, out of total # of single-end reads
- Duplicates: # of duplicated read pairs
- % Duplicates: % of duplicated read pairs, out of all read pairs
- Unique valid pairs: HiC read pairs which are not derived from artifacts such as self-circles and dangling-ends, and which contain spatial proximity information
- %Unique valid pairs: % of unique valid read pairs, out of all read pairs
- Library Complexity: Theoretical # of unique molecules in a Hi-C library.
- INTRA pairs: All unique pairs where both read-ends align to the same chromosome
- % INTRA pairs: % of all unique total pairs that have both read-ends aligning to the same chromosome
- INTRA >15kb pairs(Lcis): All unique pairs where both read-ends align to the same chromosome and have an insert size >=15kb
- % INTRA >15kb pairs(Lcis): Intra_ge_15kb_pairs: % of all unique total pairs that have both read-ends aligning to the same chromosome and have an insert size >=15kb
- INTER pairs(Trans): All unique pairs where each read-end aligns to a different chromosome
- Lcis_trans_ratio: The ratio of Lcis to Trans data. This is the signal to noise ratio for translocation calling.
- SVs: # of SV calls made by the Arima SV Pipeline