Advanced Options

The XML file allows the user to set a number of additional options, which are outlined here.  You can see how they are entered based on this example file.  (note that in the example file each option has a type attribute which should not be edited).  Note that editing XML is very easy with a good editor such as XML Notepad.

OutputFileNamePrefix - The results are output in a file with this name plus a ".csv" suffix.

Verbose - Produces messages during analysis. (True/False)

RequireM13Sequence - Check for the presence of the M13 program. (True/False)

AssignImperfectlyMatchedReads - Reads that are not a perfect match to a barcode and type can be assigned if a Smith-Waterman-Gotoh alignment in the program determines that they are close enough to one of the types of sequences being looked for.  Setting this to true can significantly increase the program length but can help recover additional data.  Default=True.  True/False.

InitialReadsToParse - Unfortunately, FASTQ files come in a variety of indistinguisable formats, so the quality scores can mean different things depending on which software produced them, and there is no way to know while parsing which format was used.  To allow AF Seq programs to still use quality scores, they pre-parse this number of reads (default=5000) to get metrics on the average QC score for a read and what an expected low value is.  Reads determined to be of very low quality based on the metrics from these initially parsed reads are not aligned to attempt to assign them, which significantly speeds ups the program by avoding junk data.

QuantileOfAvgReadQualityCutoff - After parsing the inital set of reads, we look at what the average QC score is for reads in the lowest quantile specified here (default=0.02 or 2%) to determine the filter.  For example, at the default settings if a reads average QC score is less than the bottom 2% of average QC scores and it is not an exact match to a barcode and a type, the program will not try to align it.  Setting this to 0% means we attempt to align all reads.

MaxPercentageNForInexactMatches - Any read where the number of 'N' characters (as opposed to 'A','C','G' or 'T') is higher than this percentage is not aligned if not an exact match.  This parameter is largely redundant with the QuantileOfAvgReadQualityCutoff parameter as both reads with many "N"s tend to be low quality reads.

MatchScore - Alignment option, value for a match, should be positive

MisMatchPenalty - Alignment option, value for a mismatch, should be negative

GapStartPenalty - Alignment option, value for Gap Start, should be negative

GapExtendPenalty - Alignment option, value for Gap Extension, should be negative

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