Help

[Federico Bernuzzi]

Dear Sir/Madame,

 

I have got some sequencing data that I would like to visualise. I used TopHat on Galaxy to align the data to the reference genome hg38 and have downloaded both the BAM and BAI files. When I launch IGV I first change the reference genome at the top from hg19 to hg 38 and then load my file from url which is saved on my desktop. After adding the file I get an error message saying “An index file required for SAM and BAM files”. I looked online to try and solve the problem and I have noticed that you require an igv.log file? What exactly is an igv.log file and where can it be obtained? I was wondering whether you could provide some additional info on how to solve the problem.

 

Many thanks for the help and apologise for any inconveniences caused

 

Sincerely

Federico Bernuzzi

[Helga Thorvaldsdottir]

Frederico,

If the files are saved on your local computer, use "Load from File" to load the .BAM file (not "load from url"). Also make sure that the .BAI file is in the same directory as the .BAM file and that both files have same name - apart from the filetype suffix. Otherwise IGV won't find the index.

Helga

[Federico Bernuzzi]

Dear Helga,

I am going to try now. Many thanks for the email, much appreciated. Hopefully it will work

Kind regards

FB

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[Federico Bernuzzi]

Dear Helga,

Just to clarify would I need to add both the BAM and BAI files? I have added the BAM files like you recommeded and that works but when I then try and add the BAI I get the following error message

Apologise for any inconviences caused. Many thanks

FB

2017-03-30 15:36 GMT+01:00 Helga Thorvaldsdottir <he...@broadinstitute.org>:

[Helga Thorvaldsdottir]

You only load the BAM file. And then IGV automatically finds the corresponding BAI file, as long is it's named correctly and is in the right directory. I see a bam track behind the error message window in your screenshot, so it looks like you're all set.

Helga

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[Federico Bernuzzi]

Many thanks

Have a pleasant evening

FB

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