Problem visualizing reference sequence

Ray G

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Apr 9, 2020, 9:02:40 PM4/9/20

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Hello,

I'm having a problem.

I want to show the reference sequence hg19, but I can't show it correctly and it appears like this attachment png file.

On the other hands, I can show the reference sequence hg38.

I use IGV_2.8.2 and Mac OS High Serra Version 10.13.6. memory is 16GB.

Could you let me know how can I solve this problem?

Thank you,

IGV2020-04-10.png

Xiao Lei

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Apr 9, 2020, 9:46:19 PM4/9/20

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seems like one problem I had, please refer to https://www.biostars.org/p/416973/#416977

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James Robinson

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Apr 9, 2020, 10:33:17 PM4/9/20

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Hi Ray, the usual reason for this is a proxy or firewall blocking access to our S3 bucket that is serving the sequence. However that bucket is the same for hg38 and hg19 so this is curious.

Could you try the following as an experiment?

(1) shutdown IGV

(2) download the following "hg19.genome" and copy it to the "igv/genomes" folder under your home directory. Then restart IGV

Alternatively, instead of 2 you can save hg19.genome anywhere then load it from the menu "Genome > load from file"

Let us know the result, and attach your igv.log file. This is located in the "igv" folder under you home directory.

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hg19.genome

Ray G

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Apr 14, 2020, 9:56:31 PM4/14/20

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Thank you for your message.

I did (2), but the problem was not improved.

And I loaded the hg19.genome file but that message was showed as "Can not determine the file type. Is it a sample information file?"

and when I selected yes or no, the problem was not solved.

I loaded the hg38.genome file in the same way and it showed correctly.

I attached my igv.log file.

Could you let me know how can I solve this problem again?

2020年4月10日金曜日 11時33分17秒 UTC+9 James Robinson:

Hi Ray, the usual reason for this is a proxy or firewall blocking access to our S3 bucket that is serving the sequence. However that bucket is the same for hg38 and hg19 so this is curious.

Could you try the following as an experiment?
(1) shutdown IGV
(2) download the following "hg19.genome" and copy it to the "igv/genomes" folder under your home directory. Then restart IGV

Alternatively, instead of 2 you can save hg19.genome anywhere then load it from the menu "Genome > load from file"

Let us know the result, and attach your igv.log file. This is located in the "igv" folder under you home directory.

On Thu, Apr 9, 2020 at 6:02 PM Ray G <gr25...@gmail.com> wrote:

Hello,

I'm having a problem.
I want to show the reference sequence hg19, but I can't show it correctly and it appears like this attachment png file.
On the other hands, I can show the reference sequence hg38.
I use IGV_2.8.2 and Mac OS High Serra Version 10.13.6. memory is 16GB.
Could you let me know how can I solve this problem?

Thank you,

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To unsubscribe from this group and stop receiving emails from it, send an email to igv-...@googlegroups.com.

igv.log

Ray G

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Apr 14, 2020, 9:59:00 PM4/14/20

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Thank you for your message.

My problem was just about reference sequence, not my fasta file.

I can not solve the problem yet.

2020年4月10日金曜日 10時46分19秒 UTC+9 Xiao Lei:

seems like one problem I had, please refer to https://www.biostars.org/p/416973/#416977

On Thu, Apr 9, 2020 at 9:02 PM Ray G <gr25...@gmail.com> wrote:

Hello,

I'm having a problem.
I want to show the reference sequence hg19, but I can't show it correctly and it appears like this attachment png file.
On the other hands, I can show the reference sequence hg38.
I use IGV_2.8.2 and Mac OS High Serra Version 10.13.6. memory is 16GB.
Could you let me know how can I solve this problem?

Thank you,

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James Robinson

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Apr 14, 2020, 10:00:01 PM4/14/20

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As noted in the instructions, you need to load the genome file from the "Genomes" menu, not the "File" menu. Please try that. If it doesn't work I'm sorry but I don't have an answer for you.

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Ray G

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Apr 17, 2020, 3:28:14 AM4/17/20

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Thank you very much for your support.

I tried "Genomes" menu, but I couldn't solve the problem.

On the other hand, hg38 was shown correctly.

I will give up for using my computer for IGV and try using another computer.

If you notice another answer for this problem, I'm glad to let me know about it.

Thank you again.

2020年4月15日水曜日 11時00分01秒 UTC+9 James Robinson:

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/aae8c99b-800b-4d79-ad9f-65a65dd192de%40googlegroups.com.

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