Difference in IGV output

[Dongjo Ban]

After going through the tutorials on github on the virtual machine, I wanted to reproduce the results in my own Linux and Mac machines.

I can't seem to replicate the result on IGV output. 

The image on the top is the output I was able to generate and below that is the output generated by the tutorial VM setup.

I understand the window size may affect how much I can see, but I can't seem to figure out the colors and etc. I couldn't seem to find any info on this on the manual on the website either. Could someone share their insight on this matter?

By the way I made sure that the view preference were the same before posting here.

Thank you.

[Dongjo Ban]

I'm sorry I forgot to post the version and the machine. 

I tried to replicate the result both on Ubuntu (Xenial) and Mac OSX (El Capitan). On the machines I couldn't seem to replicate the IGV results, the version if IGV was 2.3.97.

[James Robinson]

Hi,  I'm sorry I don't know what you are referring to wrt "tutorials on the virtual machine".   What github repository are your refering to,  and what virtual machine?   

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[Dongjo Ban]

https://github.com/trinityrnaseq/RNASeq_Trinity_Tuxedo_Workshop/wiki/Tuxedo-Genome-Guided-Transcriptome-Assembly-Workshop

I apologize for any confusion. The tutorial above was the one I was talking about. 

Thanks.

On Wednesday, September 6, 2017 at 6:17:49 PM UTC-4, Jim Robinson wrote:

Hi,  I'm sorry I don't know what you are referring to wrt "tutorials on the virtual machine".   What github repository are your refering to,  and what virtual machine?   

On Wed, Sep 6, 2017 at 3:16 PM, Dongjo Ban <dongj...@gmail.com> wrote:

I'm sorry I forgot to post the version and the machine. 

I tried to replicate the result both on Ubuntu (Xenial) and Mac OSX (El Capitan). On the machines I couldn't seem to replicate the IGV results, the version if IGV was 2.3.97.

On Wednesday, September 6, 2017 at 6:14:19 PM UTC-4, Dongjo Ban wrote:

After going through the tutorials on github on the virtual machine, I wanted to reproduce the results in my own Linux and Mac machines.

I can't seem to replicate the result on IGV output. 

The image on the top is the output I was able to generate and below that is the output generated by the tutorial VM setup.

I understand the window size may affect how much I can see, but I can't seem to figure out the colors and etc. I couldn't seem to find any info on this on the manual on the website either. Could someone share their insight on this matter?

By the way I made sure that the view preference were the same before posting here.

Thank you.

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[James Robinson]

That's not our repository,  so you'll have to pose you question to the owner.  

Just looking at your screenshots,  the bottom one looks like the alignments are colored by strand and "squished".    Its possible they are colored by first-of-pair strand.   Right-click and "squish" your alignments then change color-by options.

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[Dongjo Ban]

Ah I see. I just wanted to know if this was just simply something I can manipulate within IGV to achieve the same output.

Thank you.

[James Robinson]

Were you able to get the same result, or something close?