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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 <br> Column 2: Total # of unique reads (i.e. if a read is repeated in the dataset, it is not counted)<br> 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)<br> Column 4: Total # of reads in the dataset<br> 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)<br> == Brown Box (QCReport using Base Quality) == Column 1: Lane #/Sample id<br> Column 2: Type of Dataset (filtered or not) (Please refer to the Solexa Sample Processing Details OR FAQ for questions on filtering)<br> Column 3: Total # of reads in the dataset with Tag/Linker <br> Column 4: PERCENT Total # of reads in the dataset with Tag/Linker <br> Column 5: Unique # of reads in the dataset with Tag/Linker (Please refer to the FAQ for questions on filtering)<br> Column 5: PERCENT Unique # of reads in the dataset with Tag/Linker (Please refer to the FAQ for questions on filtering)<br> == Green Box (QCReport using Base Quality) == Column 1: Position on the Reads<br> Column 2: Total # of Adaptor/Linker/ Reads Starting at Position specified in column 1<br> Column 3: PERCENT Total # of Adaptor/Linker/ Reads Starting at Position specified in column 1<br> == Blue Box (QCReport using Base Quality) == Column 1: Lane #/Sample id<br> Column 2: Total # of Adaptor Reads<br> Column 3: PERCENT Total # of Adaptor Reads<br> Column 4: Total # of PolyA Reads<br> Column 5: PERCENT Total # of PolyA Reads<br> == Grey Box (QCReport using Base Quality) == Column 1: Lane #/Sample id<br> Column 2: Type of Dataset (filtered or not) (Please refer to the FAQ for questions on filtering)<br> 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)<br> == Purple Box (QCReport using Base Quality) == Column 1: Lane #/Sample id<br> Column 2: Type of Dataset (filtered or not) (Please refer to the FAQ for questions on filtering)<br> Column 3 and further: Percentage of bases with a quality score of atleast 20 in that cycle/position.<br> == 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.

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