Ask Your Question
0

Trouble loading BAM files

asked 2012-09-26 14:11:18 -0600

David Hawkes gravatar image

The software looks good but I am having trouble loading my own BAM files. I get the error "Could not find reference sequence for current build". The BAM should be fairly standard and was built to the current human genome. Do you know what this is likely to be and how to solve it?

edit retag flag offensive close merge delete

7 answers

Sort by » oldest newest most voted
0

answered 2013-06-19 06:02:01 -0600

Pooja Singh gravatar image

Hi Jami,

I am working with the Eucalyptus grandis, JGI1.1 build. My BAM file has the chromosomes labeled as scaffold1 ; scaffold_2 and so on. I would appreciate it if you could email the instructions to me. I don't really want to wait until the next release for the solution of the problem.

Thanks,

Pooja pooja.singh09@gmail.com

edit flag offensive delete link more
0

answered 2013-06-12 16:39:24 -0600

Hi Pooja,

To be able to correctly recognize the genome and build of your BAM files GenomeBrowse requires that the corresponding assembly file for the build contain the recognized "names" of the chromosomes so the correct reference sequence can be used to compute the index and coverage files necessary for plotting.

Fixing Gabriel's issue required that we edit the provided assembly file for the sheep (OAR3.1) genome so that it included OAR1, OAR2, etc. as acceptable names for the chromosomes, we then shipped that version of the assembly file with the next release of GenomeBrowse. So the fix was specific to his issue and not universal to all genomes.

If you could provide the species and build for your data we can provide you with an adjusted assembly file to see if that fixes your issue. I can also provide instructions on how you can make these edits yourself if you would prefer.

Thanks, Jami...

edit flag offensive delete link more
0

answered 2013-06-12 09:38:16 -0600

Pooja Singh gravatar image

updated 2013-06-12 09:43:07 -0600

Hi Jami. I am having the same problem. I think it is because my BAM file has the chromosomes labelled as scaffold1, scaffold2 and so on instead of chr1, chr2...like the reference file from phytozome. You guys said you sorted out the problem in the latest release of the software, which is the one I have (1.1.2). So why as I still getting the error (error code 18)? Please help!

Pooja

edit flag offensive delete link more
0

answered 2013-03-27 09:51:31 -0600

Gabriel,

We determined the error was occurring due to an incompatibility issue with the way chromosomes where being labeled. GenomeBrowse expected the chromosomes in the form Chr1, Chr2, etc. and in your BAM files they were labeled OAR1, OAR2, etc. We have updated GenomeBrowse to accept alternate labeling formats.

Please update to the most recent version of GenomeBrowse to access all available features. To update GenomeBrowse please download the installer from our website.

Thanks, Jami...

edit flag offensive delete link more
0

answered 2012-10-12 13:01:08 -0600

I have the same problem with Ovis aries OAR_2.0. I downloaded the appropriate sequence but it didn’t work

edit flag offensive delete link more
0

answered 2012-10-12 13:00:42 -0600

I have the same problem with Ovis aries OAR_2.0. I downloaded the appropriate sequence but it didn’t work

edit flag offensive delete link more

Comments

Gabriel, I'm sorry to hear you are having troubles. Did GenomeBrowse crash when you attempted to load the file? Would you be willing to share the file with us? Please email us at genomebrowse@goldenhelix.com if you would be willing to share the BAM file in a secure fashion.

Jami Bartole ( 2012-10-15 16:10:59 -0600 )edit
0

answered 2012-09-26 16:33:27 -0600

You will first need to download the appropriate reference sequence track from the annotations server to your local computer. From the Add menu choose the appropriate sequence for the species and build corresponding to your data and select Download. Once the download is complete you should be able to load in your BAM file.

edit flag offensive delete link more
Login/Signup to Answer

Questions should be tagged FeatureRequest for asking about a non-existing feature or proposing a new idea, GeneralInquiry for general questions about GenomeBrowse or directions on how to do something, or RanIntoProblem if you want to report an issue or had difficulty getting to an expected result.

Question Tools

Follow
1 follower

Stats

Asked: 2012-09-26 14:11:18 -0600

Seen: 531 times

Last updated: Jun 19 '13