Hello, everyone!
I have a questoin: field 11 in export.txt files (illumina pipeline output) contains chromosome match name OR code indicating reason for no matching. I wonder if someone knows more about these codes: NM means no match, QC means too many Ns (I'm told) but what about codes like 0:1:0??
I want to remap the reads using bowtie but am not sure which ones to retain. Are there some codes that indicate 'definitely do not use these reads' (QC comes to mind) or can I use ALL reads and the information in quality scores will take care of this (given appropriate bowtie settings)?
I ask because my impression so far with regards to reads 'passed filtering' is that they only passed filtering because the criterion (FAILED_CHASTITY<=1.00) was satisfied and I don't feel that failure to pass this one criterion is enough to disqualify a read... Are there other criteria that also determine failure to pass filter (this seems to be the default one, used by person who ran machine I got data from)?
Thanks a lot!!!!
I have a questoin: field 11 in export.txt files (illumina pipeline output) contains chromosome match name OR code indicating reason for no matching. I wonder if someone knows more about these codes: NM means no match, QC means too many Ns (I'm told) but what about codes like 0:1:0??
I want to remap the reads using bowtie but am not sure which ones to retain. Are there some codes that indicate 'definitely do not use these reads' (QC comes to mind) or can I use ALL reads and the information in quality scores will take care of this (given appropriate bowtie settings)?
I ask because my impression so far with regards to reads 'passed filtering' is that they only passed filtering because the criterion (FAILED_CHASTITY<=1.00) was satisfied and I don't feel that failure to pass this one criterion is enough to disqualify a read... Are there other criteria that also determine failure to pass filter (this seems to be the default one, used by person who ran machine I got data from)?
Thanks a lot!!!!
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