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.
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:
bam datasets to the target Galaxy server. Confirm the transfers are successful and complete. FAQs: https://galaxyproject.org/support/
Thanks! Jen, Galaxy team
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
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