SequencingQC - Revision history

Sgupta at 17:14, 10 November 2011

2011-11-10T17:14:54Z

Sgupta at 17:13, 10 November 2011

2011-11-10T17:13:57Z

Sgupta at 17:13, 10 November 2011

2011-11-10T17:13:27Z

Sgupta at 18:28, 7 January 2011

2011-01-07T18:28:26Z

New page

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 =

{| class="wikitable" style="font-style:italic; font-size:120%; width:100%; border:2px solid white; height:100px" align="center"
|-
| [[image:QualityReport.jpg|QCReport using Base Quality|center|thumb|500px]]
|
| [[image:ELAND_QC.JPG|ELAND based QC|center|thumb|500px]]
|-
|}

== 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 [http://jura.wi.mit.edu/genomecorewiki/index.php/Sumeet_Gupta#Do_we_filter_.22bad.22_reads_from_the_final_dataset.3F_.5B06.2F19.2F09.5D| FAQ] for questions on filtering) 
Column 4: Total # of reads in the dataset 
Column 5: Total # of reads IN FILTERED READS (Please refer to [http://jura.wi.mit.edu/genomecorewiki/index.php/Sumeet_Gupta#Do_we_filter_.22bad.22_reads_from_the_final_dataset.3F_.5B06.2F19.2F09.5D| 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.

← Older revision		Revision as of 17:14, 10 November 2011
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	== '''''Sequencing Quality Control Based On FASTQ (Basecalls and quality scores)''''' \|\| '''''[[ELANDQC\|Go to Sequencing Quality Control Based On ELAND Alignments]]''''' ==		== '''''Sequencing Quality Control Based On FASTQ (Basecalls and quality scores)''''' \|\| '''''[[ELANDQC\|Go to Sequencing Quality Control Based On ELAND Alignments]]''''' ==

−	[[Image:~~WIGTC-2011-retreat-poster~~.jpg]]	+	[[Image:FASTQ_QC.jpg]]

@@ Line 1: / Line 1: @@
 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.
-== '''''Sequencing Quality Control Based On FASTQ (Basecalls and quality scores)''''' ==
+== '''''Sequencing Quality Control Based On FASTQ (Basecalls and quality scores)''''' || '''''[[ELANDQC|Go to Sequencing Quality Control Based On ELAND Alignments]]''''' ==
 [[Image:WIGTC-2011-retreat-poster.jpg]]