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Problem downloading BAM file

asked 2013-02-25 10:18:53 -0600

Alexandra Ortolaza gravatar image

I am having issue downloading my bam files of human exome data. I am getting error: aligned reads are not sorted. error code 3 and the sample files asked for GRCH37g1k and I managed to succesfully download that track.

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answered 2013-02-25 11:51:39 -0600

Alexandra Ortolaza gravatar image

Thank you Jami for that information. I will work on trying to sort them.

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answered 2013-02-25 11:47:30 -0600

Hi Alexandra,

Unfortunately GenomeBrowse is not able to handle unsorted BAM files. We recommend using SAMtools or a similar BAM tool to have the file sorted.

Once the file is sorted GenomeBrowse will be able to successfully compute index and coverage files for viewing the BAM file since you have download the corresponding reference sequence.

Let us know if you have any further questions or issues.

Thanks, Jami...

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Asked: 2013-02-25 10:18:53 -0600

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Last updated: Feb 25 '13