Question: merging BAM files from within a list of datasets
gravatar for muhgi
3.4 years ago by
United States
muhgi0 wrote:

I uploaded three pairs of pairwise FASTQ files and combined them into a paired dataset list. Then I did some processing and ended up with a list of datasets--three BAM files. I want to merge the three BAM files into one. I tried to use BAMTools Convert, Merge, Randomize, but this does not appear to be working--no processing or change for an hour. It also looks like it is still creating three BAM files in a list, not one.

How do I get these BAM files combined? There is very little to no documentation for datasets...


galaxy dataset • 1.1k views
ADD COMMENTlink modified 3.3 years ago by Jennifer Hillman Jackson25k • written 3.4 years ago by muhgi0
gravatar for Jennifer Hillman Jackson
3.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:


This particular tool does not have the functionality to process individual components of a collection together as a group. I created a Trello ticket for the usage request:

Another route would be to unpack the collection then process the individual datasets using the "multiple datasets" input option. However, unpacking a dataset collection is most likely a function that has not yet been enabled in the Galaxy user interface (I do not personally know how to do this). I requested the functionality in this Trello ticket, although it may exist elsewhere, as this is a known desired function.

Please follow the tickets for updates from the developers. Our team may also comment further directly here.

Dataset collections are undergoing rapid and active development at this time. Once this stabilizes, more documentation will be created.

Thanks for reporting the use case! Best, Jen, Galaxy team


ADD COMMENTlink written 3.3 years ago by Jennifer Hillman Jackson25k
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