Hai Galaxy Team,
I have created a .sam file using my own tool. I used a custom genome that I
added to the bowtie_indices.loc.
I want to create another tool which will contain 3 steps,
1. samtool view (sam to bam conversion)
2. samtool sort (sorting bam file)
3. samtool index (creating .bai file)
My problem is how the galaxy can know about the index(.bai) file I am creating?
>From one of the mailing list I learn that a bai file is automatically created
>when adding a bam file to the history.
So can I skip the 3rd step(samtool index)?
ie,Whether a .bai file will create automatically when the tool create the
sorted bam file?
If yes,where will be the .bai file?
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at: