Which means the default library orientation?

Question

[lee.jingu0626]

Hi.

I have one question when I study about DELLY paper.

(DELLY: structural variant discovery by integrated paired-end and split-read analysis.)

In paper, DELLY(tool of detecting Structural variation) records non-mapped read one alignment direction, which can be inferred from the mapped read and the default library orientation.

I wonder the default library orientation. Is it the default value in DELLY tool or commonly used for detecting SV?

Answer 1

[Ashutosh Pandey]

DELLY computes the default read-pair orientation and the paired insert size using the input BAM file. In paired-end libraries, the two mates can come from the opposite strand (Illumina) or the same strand (SOLiD). DELLY will determine the read-pair orientation and paired insert size for you and you dont have to worry about providing these information. It will then identify discordantly mapped read-pairs that either have an anomalous orientation or an insert size greater than the expected range to detect SVs.