Overlaying bedgraph/bigwig tracks

[Varun Gupta]

HI JIm,
I am trying to overlay 3 bedGraph/bigWig tracks. I have made the tracks in a way that they do not coincide at the same nucleotide. When overlaying 2 things happen(I have done group autoscaling)

1. The intensity of the colors after overlaying the tracks goes down(they do not coincide)
2. I cannot see the data-range even though the box is checked.

Also on a separate note, I have the bam files for the 3 samples and I want to overlay the read tracks so that each sample has a different color of reads. Can this be done? If not is there a way I can combine the 3 bam files in one and somehow provide a particular color to the alignment of each sample so that when I load it in IGV , it shows 3 different colors over a region??

Thanks for all the help..

Regards
Varun

[James Robinson]

Hi,  I'll look into this but it will be the end of the week.    WRT intensity of the colors,  I'm not sure what you are referring to but if you overlay tracks they are drawn with some transparency (alpha).

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[Varun Gupta]

Hi JIm,
Thanks for the reply. Yes wrt Intensiy, after overlaying the tracks they are drawn with some transparency, but that would work.

Also I was thinking for 3 separate bam files, I can add 3 different read groups and then see If I can color it according to read groups. Just a thought.

Hope to hear from you over the weekend.

Regards
Varun

On Wednesday, January 17, 2018 at 10:28:04 AM UTC-5, Jim Robinson wrote:

Hi,  I'll look into this but it will be the end of the week.    WRT intensity of the colors,  I'm not sure what you are referring to but if you overlay tracks they are drawn with some transparency (alpha).

On Tue, Jan 16, 2018 at 2:00 PM, Varun Gupta <gupta5...@gmail.com> wrote:

HI JIm,
I am trying to overlay 3 bedGraph/bigWig tracks. I have made the tracks in a way that they do not coincide at the same nucleotide. When overlaying 2 things happen(I have done group autoscaling)

1. The intensity of the colors after overlaying the tracks goes down(they do not coincide)
2. I cannot see the data-range even though the box is checked.

Also on a separate note, I have the bam files for the 3 samples and I want to overlay the read tracks so that each sample has a different color of reads. Can this be done? If not is there a way I can combine the 3 bam files in one and somehow provide a particular color to the alignment of each sample so that when I load it in IGV , it shows 3 different colors over a region??

Thanks for all the help..

Regards
Varun

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