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We have done some RNA-Seq on Arabidopsis T-DNA lines and mapped the reads on to Arabidopsis genome. Now we wanted to confirm the T-DNA deletion of those lines by loading them on IGV. As a control we also wanted to load T-DNA lines as tracks on IGV to make sure that the T-DNA lines we chose were correct. I am wondering where can i get bam files for those confirmed T-DNA lines?

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  • $\begingroup$ Sorry I might be missing something. You mentioned mapping the reads onto the genome. The output is a bam file right? You can just create an index for it and load it into IGV $\endgroup$
    – StupidWolf
    Commented Oct 24, 2019 at 9:10
  • $\begingroup$ Are you asking how to see the location and names of all the T-DNA lines, like shown here? $\endgroup$
    – Lynn
    Commented Oct 24, 2019 at 20:00

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