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BAM file upload

asked 2013-07-29 11:08:28 -0700

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Hi, We have the human cell line Hiseq RNA-seq data. The facility helped us to do the Tophat and sent us back the bam and bed file. I tried to upload the bam file to the Genomebrowser, and it always shows the wrong information " The *bam.gz" is not recognized as having a supported data format and can not be added. Sorry i am new to the RNA-seq analysis and the GB, and maybe i will have a lot questions in the future. Thanks.

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Hi, Jami: Thanks for the answer. After unzip, I can upload the file; But the Coverage and Pile-up shows " Data is unavailabe at this zoom level". By the way, can i have your email address? I can ask your questions directly. Thanks. Haiyan

Haiyan Lei ( 2013-07-31 12:55:23 -0700 )edit

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answered 2013-08-01 08:30:45 -0700

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Haiyan,

If GenomeBrowse does not recognize the species and build of the data in your BAM file then the software will be unable to compute the coverage file necessary to view the BAM file on a genome wide scale. If you have an existing BAI file in the same directory as the BAM file then GenomeBrowse can read the data for small zoomed in regions and once you get outside of the allowed region you will receive the "Data is unavailable at this zoom level" message.

What species and build is the data in your BAM file? If it is for one of our supported genomes then it is possible the BAM file has some unexpected formatting that is causing issues with our system. If you click on the BAM file and then look in the data Console and scroll to the bottom of the window you will see the header information for the BAM file, if you could provide me with this information I can take a look and see what is going wrong.

You can email this information to me at genomebrowse@goldenhelix.com.

Let me know how I can assist you further.

Thanks, Jami...

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answered 2013-07-31 12:51:43 -0700

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Hi, Jami:

Thanks for your answer. After unzip, i can upload the data. But for the Coveragae and Pile-up, the screen shows " Data is unavailabel at this zoom level.". Thanks.

Haiyan

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answered 2013-07-29 16:42:03 -0700

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Hi Haiyan,

We are happy to answer any questions you may have about GenomeBrowse.

GenomeBrowse is unable to read compressed BAM files (*.bam.gz). You will first need to unzip the file and once that is complete you should be able to load the *.bam file into GenomeBrowse without errors.

Please let us know if you have any further issues.

Thanks, Jami...

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Asked: 2013-07-29 11:08:28 -0700

Seen: 39,780 times

Last updated: Aug 01 '13