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What biologically and technically orphaned reads do mean?
Is in term of quality the orphan reads should be discarded from data?
Is in term of quality the orphan reads should be discarded from data?
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__Bach__ -
Are you referring to read(s) that you are unable to map back to a reference that you know they *should* map to? -
After quality or adapter trimming paired-end reads, one of the pairs may be discarded and the remaining read is often referred to as an orphaned read.Comment
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That can be the "technical" orphan.
If it does not match a reference it is supposed to then does that make it a "biological" orphan?Comment
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I Think so, if this single read (forward or reverse) does not have a similar in a reference database, it could be a biological orphan, but it might be a unknown sequence form the "unseen majority"
what I am not understanding, why does the paired end technology of Illumina produce these "technical orphan"? is it a matter of coverage? or library enrichment?
thanks four your replies
Originally posted by GenoMax View Post__Bach__Comment
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It is not the technology that produces these technical orphans, but treatment of the data. If you have a forward and reverse read of a single pair and the forward read has low quality and/or adapter sequence, you would remove that sequence from the set. That would leave the reverse sequence as a "technical" orphan, if that is what we are calling it.Originally posted by Bachbioinfo View PostComment
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Thanks, I catch it, is a matter of data treatment and quality filter
My question was so naive, I did not pay attention for the data source whether are filtred or not. Excuse me for this kind of questions and thanks for clarifying__Bach__Comment
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