Download and Extract Reads in BAM

[Shailesh_Kumar_Dhuda]

This tools seem to be wonderful, however usually BAM or SAM file is aligned with our specified references sequence, but here we do not get option to select which reference sequence you want to opt or even just selecting SRA and with whom it will align, I am not sure ?

Thank you very much.

[jennaj]

Welcome, @Shailesh_Kumar_Dhuda

You can map against any reference genome in Galaxy. You’ll need to source the fasta, load it into a Galaxy history, then choose the “from the history” option on the tool form.

Please start here → Custom genome + custom build: How to use a genome that is not natively indexed at the server you are working at - #2 by jennaj

For loading the reference genome fasta, you can usually just copy/paste the file URL from a public source into the Upload tool. Or, locally browse and file on your computer and load the file that way.

• Getting Data into Galaxy

Then, for mapping in general, please see the tutorials here to start with.

• Using a reference genome index already on the server → Hands-on: Mapping / Mapping / Sequence analysis
• Using a reference genome fasta from the history → Hands-on: SARS-CoV-2 Viral Sample Alignment and Variant Visualization / SARS-CoV-2 Viral Sample Alignment and Variant Visualization / Sequence analysis

If you haven’t used Galaxy before, we have some simple “first time” tutorials here, too.

• Introduction to Galaxy Analyses / Tutorial List

If I misunderstood what you are trying to do, or you need detailed help, please explain a bit more please.