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We have some RNA from knock-in mice, there are two different sequences we're looking for. We have aligned to the mouse genome using STAR but the sequence isn't there which isn't too surprising What is the best way to check for the presence of the sequence? Should I just turn them into a sequence and use them as the reference genome for STAR to align to? Is there a way I can easily incorporate it into the existing genome so I could get read counts for everyhting including those reads? Should I just BLAST using something like magicblast?

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  • $\begingroup$ Please search biostars.org, this has been asked before and discussed there. I think the naive approach is to include the sequences as extra chromosomes, then extract reads mapping to it and then check the soft-clipped part of the reads (that actually come from the genomic neighborhood) and see whether you can track it back to get a proxy for the insertion site. $\endgroup$
    – user3051
    Nov 5, 2020 at 11:44
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    $\begingroup$ Depends on the throughput. High throughput download the mouse genome and use Blat (a bit out of date now)? Megablast just make sure you select the mouse genome to speed the blasting. $\endgroup$
    – M__
    Nov 5, 2020 at 12:25
  • $\begingroup$ @ATpoint could you give me some suggestions on what to search by any change? I couldn't really find anything useful partly because it kept talking about Indels. $\endgroup$
    – Sethzard
    Nov 6, 2020 at 15:33
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    $\begingroup$ @Michael I'll look into that. Thanks. $\endgroup$
    – Sethzard
    Nov 6, 2020 at 15:34
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    $\begingroup$ @Sethzard biostars.org/p/374583 $\endgroup$
    – user3051
    Nov 7, 2020 at 9:39

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