How to confirm the exact integration site for "span" reads

[20182531027]

HI, thanks for your wonderful/excellent software.
And I have one question, maybe you can give me some ideas, there are two types of reads that can be used to find the integration sites for PE reads, one is "split", the other is "span", and how does the software confirm the exact integration sites for the span reads?
for the span reads, one reads was merely aligned to virus or human, the other reads was merely aligned to human or virus, the exact integration sites are uncertain, and many researches discarded this kind of reads. can you be kind enough to tell us how ctat_vif achieved that ?

[brianjohnhaas]

Hi, For the spanning reads, you're correct in that the integration site isn't known. It looks like the current release reports coordinates based on just an example paired-end set of reads, so the inner bounds of those alignments. In the next release (based on the current devel code being tested), we report the coordinates according to the inner boundaries of the available read coverage for all spanning evidence supporting the insertion. best, ~b

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On Wed, Apr 27, 2022 at 5:31 AM 20182531027 ***@***.***> wrote: HI, thanks for your wonderful/excellent software. And I have one question, maybe you can give me some ideas, there are two types of reads that can be used to found integration sites for PE reads, one is "split", the other is "span", and how does the software confirm the exact integration site for the span reads? for the span reads, one reads was merely aligned to virus or human, the other reads was merely aligned to human or virus, the exact integration sites are uncertain, and many researches discarded this kind of reads. can you be kind enough to tell us how ctat_vif achieved that ? — Reply to this email directly, view it on GitHub <#44>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKXYP25PYDZBB56L4JRDVHECOJANCNFSM5UOQAAAA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>