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Old 09-22-2013, 12:28 PM   #1
upendra_35
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Default How to add Arabidopsis T-DNA lines as tracks on IGV

Hi,
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 (to make sure that we didn't mess up the samples during sample and library preparation) 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?

Thanks Upendra
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Old 09-22-2013, 01:18 PM   #2
chadn737
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I don't think there are any bam files for these. Most of the T-DNA lines early on were mapped using PCR or cloning based methods. Only recently has the Ecker lab started doing sequencing to identify them.

What I would do, depending on how many lines you have, is check the expression of the gene knockout in each line and see if it is being expressed or not. Depending on where the insertion is, you might also see a bias toward the start of the gene if the insertion is in the coding sequence versus upstream in the promoter region.

Last edited by chadn737; 09-22-2013 at 01:20 PM.
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Old 09-22-2013, 06:05 PM   #3
upendra_35
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Hi chadn737,

In the absence of these bam files, is there any alternative exists to confirm our mutants before we start our anlaysis.

Thanks
Upendra
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