Revision as of 20:23, 19 June 2009

Note: We do not remove the reads that are suppose to be filtered by the solexa pipeline in version 1.4. However, reads suppose to be filtered are marked using a binary system of 1 = Good/Not Filtered and 0 = Bad/Filtered within the read ID. This information is in the quality score/FASTQ files.

QCReport Format

QCReport using Base Quality

ELAND based QC

Yellow Box (QCReport using Base Quality)

Column 1: Lane #/Sample id
Column 2: Total # of unique reads (i.e. if a read is repeated in the dataset, it is not counted)
Column 3: Total # of unique reads AFTER FILTERING (Please refer to FAQ for questions on filtering)
Column 4: Total # of reads in the dataset
Column 5: Total # of reads IN FILTERED READS (Please refer to FAQ for questions on filtering)

Brown Box (QCReport using Base Quality)

Column 1: Lane #/Sample id
Column 2: Type of Dataset (filtered or not) (Please refer to the Solexa Sample Processing Details OR FAQ for questions on filtering)
Column 3: Total # of reads in the dataset with Tag/Linker
Column 4: PERCENT Total # of reads in the dataset with Tag/Linker
Column 5: Unique # of reads in the dataset with Tag/Linker (Please refer to the FAQ for questions on filtering)
Column 5: PERCENT Unique # of reads in the dataset with Tag/Linker (Please refer to the FAQ for questions on filtering)

Green Box (QCReport using Base Quality)

Column 1: Position on the Reads
Column 2: Total # of Adaptor/Linker/ Reads Starting at Position specified in column 1
Column 3: PERCENT Total # of Adaptor/Linker/ Reads Starting at Position specified in column 1

Blue Box (QCReport using Base Quality)

Column 1: Lane #/Sample id
Column 2: Total # of Adaptor Reads
Column 3: PERCENT Total # of Adaptor Reads
Column 4: Total # of PolyA Reads
Column 5: PERCENT Total # of PolyA Reads

Grey Box (QCReport using Base Quality)

Column 1: Lane #/Sample id
Column 2: Type of Dataset (filtered or not) (Please refer to the FAQ for questions on filtering)
Column 3: Percentage of bases with a quality score of atleast 20 (i.e. the probability of base call being incorrect is 1 in a 100)

Purple Box (QCReport using Base Quality)

Column 1: Lane #/Sample id
Column 2: Type of Dataset (filtered or not) (Please refer to the FAQ for questions on filtering)
Column 3 and further: Percentage of bases with a quality score of atleast 20 in that cycle/position.

Yellow Box (ELAND based QC)

Column 1: Files Column 2: Genome Used Column 3: Total Reads Column 4: Reads Kept (Column 3 - Column 5) Column 5: Solexa Linker(Reads Removed) Column 6: % Removed Column 7: # of Reads that align Unique Column 8: % of Reads that align Unique Column 9: # of Reads fail to align because of too many N's Column 10: % reads w/ many N's Column 11: Reads with Multiple Matches Column 12: % reads w/ multi-match Column 13: Reads with No Match Column 14: % reads w/ no-match

Green Box (ELAND based QC)

Break down of the unique reads in U0, U1, U2.... and so on.

Blue Box (ELAND based QC)

PERCENT Break down of the unique reads in U0, U1, U2.... and so on.

Brown Box (ELAND based QC)

Number of mismatches at each position i.e. for a 36 base run, number of mismatches for position 1, position 2 ... and so on to position 36.

Grey Box (ELAND based QC)

PERCENT mismatches at each position i.e. for a 36 base run, PERCENT mismatches for position 1, position 2 ... and so on to position 36.