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Old 04-23-2019, 09:05 PM   #1
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Location: NZ

Join Date: Mar 2017
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Default Stranded library IGV

Hi all,
Could someone please explain the "color by first-in-pair" in IGV which was suggested by Jim Robinson in this post:

My understanding is if you have used a stranded library (which I have) and you tick the 'color by first-in-pair' then if the reads are red, the transcript is being transcribed from the negative strand and if they are blue, the transcript is being transcribed from the positive strand (as suggested in the post) which I have an example of in the first two images of the attached file.

Can someone clarify that if you have both blue and red reads (like in the third image of the attached file) then both stands are being transcribed??

I have tried and tried to find an answer to this such as here but I haven't found a thread that gives a precise answer and there is NO information in the IGV manual.

Many thanks.
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igv, stranded rna-seq

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