Question: how to convert tgz file to bam: Uncompressing an archive
0
gravatar for manubiomed20
21 days ago by
manubiomed200 wrote:

I just managed to download my folder with my bam files in tgz format, but I need to convert to bam, because the program only accepts this format.

archive uncompress galaxy tgz • 59 views
ADD COMMENTlink modified 21 days ago • written 21 days ago by manubiomed200
0
gravatar for Jennifer Hillman Jackson
21 days ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

What you have right now is an archive that contains one or more files (your bam data). Unpack the archive then use FTP Upload to get the bam datasets into Galaxy. You only need to upload the bam files not the .bam.bai indexes. Galaxy will coordinate sort the data and create indexes.

Steps:

  1. Unpack the archive. More details in this post or you can do your own web search with "unpack tgz" for much more online help.
  2. Use FTP to transfer the bam datasets to the target Galaxy server. Confirm the transfers are successful and complete.
  3. Use the Upload tool within Galaxy to move the FTP'd files into a history as datasets.

FAQs: https://galaxyproject.org/support/

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 21 days ago • written 21 days ago by Jennifer Hillman Jackson25k
0
gravatar for manubiomed20
21 days ago by
manubiomed200 wrote:

do not think I expressed myself in the best way. I used Glaxy to remove the duplicate reads, after this process I obtained several BAM files, but I need to export to my computer. I tried to export history, but I could not, I had to leave the story accessible and I could not do that. I was able to download, but in tgz format. the problem is that I need to export to other software, but I can not get this format tgz, the software does not accept. Thanks

ADD COMMENTlink written 21 days ago by manubiomed200

Ok, thanks for clarifying. You have a dataset collection downloaded. It can be unpacked/uncompressed using the same command and all the bams will be inside it.

Depending on what utilities are installed on your computer, you might be able to just double click on the archive to uncompress it. Or you can install a utility. Try the google search, you'll find those that are for your OS and open source without too much hunting.

If you are familiar with the command-line, this is an example using the OSX Terminal program (every MAC includes it by default). I started in the directory where the archive is located.

Note that I put single quotes around the original file name since it includes a space.

$ ls
20_ BAM-list.tgz
$ tar -xzf '20_ BAM-list.tgz'
$ ls
20_ BAM-list.tgz    BAM-list
$ cd BAM-list
$ ls
sample1.bam sample1.bam.bai sample2.bam.bam     sample2.bam.bam.bai
ADD REPLYlink modified 21 days ago • written 21 days ago by Jennifer Hillman Jackson25k
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