Question On Uploading And Use .Bam Files

Question: Question On Uploading And Use .Bam Files

5.0 years ago by

United States

Dear Sir or Madam, Recently I was trying to use Galaxy for my data analysis but ran into problems..... Condition: I used galaxy server at PSU. I tried load local .bam file directly to galaxy, I also tried FTP, but both ways resulted into the same outcome. The .bam files I was using are pure .bam files with no index. Problems: 1.After I load them, the file was recognized as .txt file, and it is "empty" (But it did take long time to upload to FTP ~1GB), in the annotation window, it shows "The uploaded binary file contains inappropriate content" 2. I tried to convert the file to .bam format, it returns "An error occurred setting the metadata for this dataset. You may be able to set it manually or retry auto-detection." Could you help me for this, I just uploaded a small file to the FTP, just in case you need it for a test. Username: ylc35@mail.missouri.edu Great thanks~ YL

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modified 5.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.0 years ago by Lu, Yuan (MU-Student) • 20

5.0 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello L.Y., I just tested .bam upload using FTP (with the client FileZilla) and all went fine. Just to confirm, you are using the public Main Galaxy server at http://usegalaxy.org? Many of our services were down for several hours yesterday for maintenance related reasons - if you upload overlapped with that all (9am-6pm EST US), you will want to do the upload again now. In my test, I did not set the datatype when I moved the file into a history, but the file was named with a ".bam" extension. In another history, I happened to have a .bam file that had a metadata detection as you describe, and when I reset, the datatype was resolved. So, given these tests done right now - I think everything is OK on the server. First, when you uploaded the file via FTP - this was confirmed to be successful? This is reported by the client tools (and command-line if using that method). Double check, as this is important. Interrupted transfers can be resumed (next time) - leave the file in the holding area, connect to the server first, then start the resume. If you are not sure of the status, maybe try again and track this, it is an important first step. Personally, I would name the file with a ".bam" extension if doing over, as this is the datatype (anyway, not just Galaxy). Second, let me show you how to reset metadata since that may also solve the issue. When the message to reset metadata comes up in an expanded dataset, this is a link. Click on it, and in the center panel the Edit Attributes form will come up. On the first, default page, near the bottom, will be a button to "detect metadata". Click on this and let the process run. If neither of these work, then you probably need to examine the contents of the .bam file to make sure it is really .bam (and only .bam). SAMTools on the line command is a good, simple choice for this. Are you able to run tools on the file? Converting to sam format will change the indexed format to one that is in plain text, if you find something off that you want to examine. You could also check with the source to see if they are aware of any problems. And not to make this overly confusing, but a transfer problem from the source to your computer could have occurred, corrupting the file. The option to upload via URL is possible if the source has the file available that way. The screencast linked from here shows all current options: http://wiki.galaxyproject.org/Support#Loading_data Please review and let us know if you continue to have problems, Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org

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