Can't see translation track.

[Jennifer Lee]

I can't see translation track. amino acid track.

Thank you for your help about reference file.

Finally, I did it.

I attach IGV screen shot.

[James Robinson]

Your sequence (fasta) has not loaded.    Did you create a .genome file or just load the fasta directly?  

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[Jennifer Lee]

Yes, I create genome file. because of our network problem hg19 can't open from server.

 

Can I open zoom in sequence and amino acid codon information/

   

    Please see that I attached file arrow position.

    Usually that position show amino acid codon and sequence marked.

    How can I open amino acid codon and sequence?  

[James Robinson]

Attach your .genome file please and I will look at it.   

On Sun, Nov 20, 2016 at 4:30 PM, Jennifer Lee <cher...@gmail.com> wrote:

Yes, I create genome file. because of our network problem hg19 can't open from server.

Can I open zoom in sequence and amino acid codon information?

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[Jennifer Lee]

I attach .genome file.

Thank you.

[James Robinson]

Is your fasta file (hg19.fa),  and fasta index file  (hg19.fa.fai)  in the same directory as your genome file?

On Sun, Nov 20, 2016 at 6:13 PM, Jennifer Lee <cher...@gmail.com> wrote:

I attach .genome file.

Thank you.

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[Jennifer Lee]

Yes, fa ,fai and .genoem  file in same directory.

2016년 11월 21일 월요일 오전 11시 15분 22초 UTC+9, Jim Robinson 님의 말:

Is your fasta file (hg19.fa),  and fasta index file  (hg19.fa.fai)  in the same directory as your genome file?

On Sun, Nov 20, 2016 at 6:13 PM, Jennifer Lee <cher...@gmail.com> wrote:

I attach .genome file.

Thank you.

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[James Robinson]

OK,  I don't know what's wrong then.   I'm sorry IGV isn't working for you.   The only final suggestion I have is to try this

(1) Load the fasta file directly from the Genomes menu  (select Genomes > Load genome from file...) and select hg19.fa

(2) Load the annotation file (refGene.txt) from the File menu  (File > Load from file...)

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[Jennifer Lee]

Please see this genome file.

After I created new reference, Human hg19.genome file created.

Please arrange to have any A,G,T,C sequence.

[James Robinson]

DId you read my previous message?  Perhpas not,  I will repeat it here.   If this doesn't work for you I think you will have to look for another program to visualize your data with.

"

OK,  I don't know what's wrong then.   I'm sorry IGV isn't working for you.   The only final suggestion I have is to try this

(1) Load the fasta file directly from the Genomes menu  (select Genomes > Load genome from file...) and select hg19.fa

(2) Load the annotation file (refGene.txt) from the File menu  (File > Load from file...)

"

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[Jennifer Lee]

No, I follow your messages and not difference between before.

AND I use IGV everyday normally until IGV update maybe Nov.2nd around.