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-   -   Question about galaxy file uploading (.bam) (http://seqanswers.com/forums/showthread.php?t=38852)

lucer105 12-02-2013 08:46 PM

Question about galaxy file uploading (.bam)
 
I was trying to load my bam files to galaxy (~1.5Gb for each of them).

After they are loaded in Galaxy, it shows the files are all empty, and the file type is .txt, and there is nothing by clicking "view data"......I tried to load the .bam files into IGV, didn't work either.... It says "could not load the index file for the .bam file, and index file is required"

I tried to convert the file type to .bam, it says "metadata could not be detected"....make sense since the files are all empty....

Any one know what to try/do?:confused:

Thanks

L

GenoMax 12-03-2013 03:06 AM

Are you uploading the files to a local galaxy mirror or to public galaxy server at PSU?

If you are using the PSU public galaxy server then "ftp upload" is the preferred method when transferring large files such as these. Instructions for that are here: http://wiki.galaxyproject.org/FTPUpload

lucer105 12-03-2013 09:35 PM

Quote:

Originally Posted by GenoMax (Post 126280)
Are you uploading the files to a local galaxy mirror or to public galaxy server at PSU?

If you are using the PSU public galaxy server then "ftp upload" is the preferred method when transferring large files such as these. Instructions for that are here: http://wiki.galaxyproject.org/FTPUpload

Thanks for offering some help.

I used galaxy server at PSU and I do use FTP....same thing.....


"1: a_accepted_hits.bam

An error occurred setting the metadata for this dataset. You may be able to set it manually or retry auto-detection.
empty
format: bam, database: mm9
The uploaded binary file contains inappropriate content"

the .bam file has no index.

GenoMax 12-04-2013 03:18 AM

If you are certain that the file you are uploading is correct then the best option would be to contact galaxy support (galaxy-user@lists.bx.psu.edu). They will generally ask you to share the file link with them and then diagnose the problem.


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