"merging BAM files from within a list of datasets"

Has this entry been addressed?:

I would like to merge three (replicate) bam files in a collection/list into a single bam file.


When I try to do this with Samtools merge, I can only select the collection but not individual bam files. And if I select the collection in which there are the bam files I see the following message.

Is there a way to see what these data 189, data 187, and data 188 are, to know what I’m merging?

Thank you!

Dear @ysrbrs,
The tool merges the data in your collection. So your file Samtools merge on data 189, 187, and 188 contains the data from your three input files SRR103*. You could not select the individual data sets, because your data is in a data set collection. In order to select your individual files (e.g., to merge just two bam files of your input data) you would need to extract the data sets from the collection with the tool Extract element identifiers of a list collection.

Have a good day and best wishes,

1 Like

Hello Florian,

Many thanks! It worked just like you explained it.

And, it will be extremely helpful to know the tool “Extract element identifiers”. Thanks for pointing it out!