IGV peak Visualation Problem
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8.8 years ago
morovatunc ▴ 550

Hello my colleagues,

I will explain my problem with two images. ( I am sorry for uploading my screen shot with a host server). I was trying to replicate the figure from one of the articles. However, When I try to replicate it, I come across with visualising peaks which seems to be in low resolution. Instead of a giving smooth concave peak, it gives odd blocks. How can I solve this problem? I guess I kind a solve it accidentally but could you comment on what is the modular way of doing this. setting etc?

not I want:

http://postimg.org/image/5xsrcmxqp/

smooth, what I did accidentally.

http://postimg.org/image/bhxp93nkz/

Thank you in advance

Best regards,
T.

ChIP-Seq IGv • 4.3k views
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How did you solve it? To me, it looks like the Y-axis binning/precision is "coarser" with the first sample, so you are seeing more steps. In particular, the difference between those two regions seems to be that there is more signal, so the Y-axis range is larger, allowing for more steps.

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Yeah, the more that I look at it, I'm guessing you scrolled a bit to the left, and since there is significantly higher signal and it's automatically scaling (you haven't specified "hard" min/max y-values), the "steps" appear smaller. You're looking at a larger range.

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Yeah, I enabled the autoscaling but what I wanted to say, I prefer to get the graphs like at the second but I get those odd ones at the first image.

  1. is getting those odd looking ones ok or makes valuable data?
  2. is there a IGV tutorial that explains those visitation setting to get a better view of the data in order to interpret results more efficient.??
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Unless you have reason to believe that the image is not accurately representing the data (or the larger biological principle), it's fine to use the more coarse "steppy" data.

I would recommend taking a look at the bigwig format (and underlying wiggle format) to get a better idea about the parameters that might affect the resolution/smoothness. Perhaps your underlying alignment data could be reprocessed with a smaller step-size, or greater precision on the track score? This will increase file size, but if you want to have the prettiest picture possible, and the underlying data support it, it might be worth remaking the wiggle.

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Sir Thank you for your help and guidance. I will comment after I apply the steps that you have mentioned.

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Hi ! I have a similar kind of problem with data visualization. I am using bam files for representation and getting steppy data, while I want curvy data as mentioned by morovatunc ..i.e. his second screen shot,is it possible without bigwig? I have bam files. Thanks

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