Assembly of the target ERV

[1577377232]

Hello，Dr. Yu,

I used IGV to check the breakpoints, and extracted the reads mapped within 150bp from TSD, assembled and aligned them.（samtools）

Is there a way to assemble a more complete ERV, via discordant reads and split reads? Because I saw in the BED file,Transposon:Start:End column,The alignment is perfect！**Such as, ERV3： 1：7525：+.**What knowledge can I learn? And what steps can I take to gradually achieve this goal?

Best,
Dan

[tianxiongbb]

Hi Dan, Unfortunately TEMP2 is not designed to assemble the insertion sequences, and I think none of the tools using normal DNA-seq data do. The start and end is inferred simply by where the reads align to the TE, if they are close to the TE start/end, it will output 1:TE_end. However, any internal truncation is undetectable which is limited by read length. Best, Tianxiong

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On Apr 25, 2024, at 9:20 PM, dan chen ***@***.***> wrote: Hello，Dr. Yu, I used IGV to check the breakpoints, and extracted the reads mapped within 150bp from TSD, assembled and aligned them.（samtools） Is there a way to assemble a more complete ERV, via discordant reads and split reads? Because I saw in the BED file,Transposon:Start:End column,The alignment is perfect！**Such as, ERV3： 1：7525：+.**What knowledge can I learn? And what steps can I take to gradually achieve this goal? Best, Dan — Reply to this email directly, view it on GitHub <#26>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFPDEDG57P3OAAJR3U5N5X3Y7GTULAVCNFSM6AAAAABGZ4NZXGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGI3DINZWGU3TGMI>. You are receiving this because you are subscribed to this thread.

[1577377232]

Thank you for your prompt reply！