Orphaned Reads from Illumina Hiseq?

[Bachbioinfo]

What biologically and technically orphaned reads do mean?
Is in term of quality the orphan reads should be discarded from data?

[GenoMax]

Are you referring to read(s) that you are unable to map back to a reference that you know they *should* map to?

[SES]

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.

[GenoMax]

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?

[Bachbioinfo]

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

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?

[SES]

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?

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.

[Bachbioinfo]

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